http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&feed=atom&action=history
BD BOX - Revision history
2024-03-29T10:48:29Z
Revision history for this page on the wiki
MediaWiki 1.41.0
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=19304&oldid=prev
Carl McBride: Slight tidy
2016-07-06T12:28:36Z
<p>Slight tidy</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:28, 6 July 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Pawel Zieliński and Joanna Trylska "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734-2744 (2011)]</ref> is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Pawel Zieliński and Joanna Trylska "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734-2744 (2011)<ins style="font-weight: bold; text-decoration: none;">]</ref> <ref>Work on BD_BOX is supported by the [https://www.ncn.gov.pl/ Polish National Science Centre</ins>]</ref> is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses [[Flexible molecules |flexible]] bead models to represent [[macromolecules]]. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened [[electrostatics]] in dielectric media and [[Lennard-Jones model |Lennard-Jones functions]]. Hydrodynamically correlated motions of particles are modeled using configuration-dependent [[diffusion]] tensors. Brownian dynamics simulations can be performed either for single molecules or [[Periodic boundary conditions |periodic]] multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses [[Flexible molecules |flexible]] bead models to represent [[macromolecules]]. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened [[electrostatics]] in dielectric media and [[Lennard-Jones model |Lennard-Jones functions]]. Hydrodynamically correlated motions of particles are modeled using configuration-dependent [[diffusion]] tensors. Brownian dynamics simulations can be performed either for single molecules or [[Periodic boundary conditions |periodic]] multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a [[Coarse graining |coarse-grained representation]] or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a [[Coarse graining |coarse-grained representation]] or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Work on BD_BOX is supported by Polish National Science Centre.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Maciej Długosz and Jan M. Antosiewicz "Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules Journal of Chemical Theory and Computation '''10''' pp. 2583-290 (2014)]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Maciej Długosz and Jan M. Antosiewicz "Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules Journal of Chemical Theory and Computation '''10''' pp. 2583-290 (2014)]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Maciej Długosz and Jan M. Antosiewicz "Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments" Journal of Chemical Theory and Computation '''10''' pp. 481-491 (2014)]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Maciej Długosz and Jan M. Antosiewicz "Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments" Journal of Chemical Theory and Computation '''10''' pp. 481-491 (2014)]</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
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Carl McBride
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=19302&oldid=prev
Carl McBride: Added some internal links
2016-07-06T11:16:52Z
<p>Added some internal links</p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:16, 6 July 2016</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <del style="font-weight: bold; text-decoration: none;"> </del>is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <ins style="font-weight: bold; text-decoration: none;"><ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Pawel Zieliński and Joanna Trylska "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734-2744 (2011)]</ref> </ins>is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses <ins style="font-weight: bold; text-decoration: none;">[[Flexible molecules |</ins>flexible<ins style="font-weight: bold; text-decoration: none;">]] </ins>bead models to represent <ins style="font-weight: bold; text-decoration: none;">[[</ins>macromolecules<ins style="font-weight: bold; text-decoration: none;">]]</ins>. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened <ins style="font-weight: bold; text-decoration: none;">[[</ins>electrostatics<ins style="font-weight: bold; text-decoration: none;">]] </ins>in dielectric media and <ins style="font-weight: bold; text-decoration: none;">[[Lennard-Jones model |</ins>Lennard-Jones functions<ins style="font-weight: bold; text-decoration: none;">]]</ins>. Hydrodynamically correlated motions of particles are modeled using configuration-dependent <ins style="font-weight: bold; text-decoration: none;">[[</ins>diffusion<ins style="font-weight: bold; text-decoration: none;">]] </ins>tensors. Brownian dynamics simulations can be performed either for single molecules or <ins style="font-weight: bold; text-decoration: none;">[[Periodic boundary conditions |</ins>periodic<ins style="font-weight: bold; text-decoration: none;">]] </ins>multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a <ins style="font-weight: bold; text-decoration: none;">[[Coarse graining |</ins>coarse-grained representation<ins style="font-weight: bold; text-decoration: none;">]] </ins>or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[http://<del style="font-weight: bold; text-decoration: none;">dx</del>.<del style="font-weight: bold; text-decoration: none;">doi</del>.org/10.<del style="font-weight: bold; text-decoration: none;">1002</del>/<del style="font-weight: bold; text-decoration: none;">jcc.21847 </del>Długosz<del style="font-weight: bold; text-decoration: none;">, </del>M.<del style="font-weight: bold; text-decoration: none;">; Zieliński, P</del>.<del style="font-weight: bold; text-decoration: none;">; Trylska, J</del>. <del style="font-weight: bold; text-decoration: none;">Brownian dynamics simulations </del>on <del style="font-weight: bold; text-decoration: none;">CPU </del>and <del style="font-weight: bold; text-decoration: none;">GPU with BD_BOX J</del>. <del style="font-weight: bold; text-decoration: none;">Comput</del>. <del style="font-weight: bold; text-decoration: none;">Chem</del>.<del style="font-weight: bold; text-decoration: none;">, 32, 2734</del>-<del style="font-weight: bold; text-decoration: none;">2744, 2011</del>]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><references/></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">;Related reading</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">*</ins>[http://<ins style="font-weight: bold; text-decoration: none;">pubs</ins>.<ins style="font-weight: bold; text-decoration: none;">acs</ins>.org<ins style="font-weight: bold; text-decoration: none;">/doi/abs</ins>/10.<ins style="font-weight: bold; text-decoration: none;">1021</ins>/<ins style="font-weight: bold; text-decoration: none;">ct500124r Maciej </ins>Długosz <ins style="font-weight: bold; text-decoration: none;">and Jan </ins>M. <ins style="font-weight: bold; text-decoration: none;">Antosiewicz "Anisotropic diffusion effects on the barnase-barstar encounter kinetics" Journal of Chemical Theory and Computation '''9''' pp. 1667-1677 (2013)]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">*[http://pubs.acs.org/doi/pdf/10</ins>.<ins style="font-weight: bold; text-decoration: none;">1021/ct300937z Maciej Długosz and Jan M</ins>. <ins style="font-weight: bold; text-decoration: none;">Antosiewicz "Transient effects of excluded volume interactions </ins>on <ins style="font-weight: bold; text-decoration: none;">the translational diffusion of hydrodynamically anisotropic molecules Journal of Chemical Theory </ins>and <ins style="font-weight: bold; text-decoration: none;">Computation '''10''' pp</ins>. <ins style="font-weight: bold; text-decoration: none;">2583-290 (2014)]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">*[http://pubs</ins>.<ins style="font-weight: bold; text-decoration: none;">acs.org/doi/pdf/10.1021/ct4008519 Maciej Długosz and Jan M. Antosiewicz "Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments" Journal of Chemical Theory and Computation '''10''' pp</ins>. <ins style="font-weight: bold; text-decoration: none;"> 481</ins>-<ins style="font-weight: bold; text-decoration: none;">491 (2014)</ins>]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase-barstar encounter kinetics J. Chem. Theory Comput., 9, 1667-1677, 2013]</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Długosz, M.; Antosiewicz, J. Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules J. Chem. Theory Comput., 10, 2583-290, 2014]</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Długosz, M.; Antosiewicz, J. Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments J. Chem. Theory Comput., 10, 481-491, 2014]</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
</table>
Carl McBride
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=19301&oldid=prev
Mdlugosz at 11:25, 5 July 2016
2016-07-05T11:25:54Z
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://www3.cent.uw.edu.pl/~mdlugosz BD_BOX Home Page]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://www3.cent.uw.edu.pl/~mdlugosz<ins style="font-weight: bold; text-decoration: none;">/#download </ins>BD_BOX Home Page]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td></tr>
</table>
Mdlugosz
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=19300&oldid=prev
Mdlugosz at 11:24, 5 July 2016
2016-07-05T11:24:10Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:24, 5 July 2016</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://<del style="font-weight: bold; text-decoration: none;">browniandynamics</del>.<del style="font-weight: bold; text-decoration: none;">org </del>BD_BOX Home Page]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://<ins style="font-weight: bold; text-decoration: none;">www3</ins>.<ins style="font-weight: bold; text-decoration: none;">cent.uw.edu.pl/~mdlugosz </ins>BD_BOX Home Page]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td></tr>
</table>
Mdlugosz
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=14412&oldid=prev
Mdlugosz at 11:58, 21 October 2014
2014-10-21T11:58:22Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:58, 21 October 2014</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <del style="font-weight: bold; text-decoration: none;">UNIQa0eb08b6ad1b2077-ref-00000006-QINU</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">UNIQa0eb08b6ad1b2077</del>-<del style="font-weight: bold; text-decoration: none;">references</del>-<del style="font-weight: bold; text-decoration: none;">00000007</del>-<del style="font-weight: bold; text-decoration: none;">QINU</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[http://dx.doi.org/10.1002/jcc.21847 Długosz, M.; Zieliński, P.; Trylska, J. Brownian dynamics simulations on CPU and GPU with BD_BOX J. Comput. Chem., 32, 2734</ins>-<ins style="font-weight: bold; text-decoration: none;">2744, 2011]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase</ins>-<ins style="font-weight: bold; text-decoration: none;">barstar encounter kinetics J. Chem. Theory Comput., 9, 1667</ins>-<ins style="font-weight: bold; text-decoration: none;">1677, 2013]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Długosz, M.; Antosiewicz, J. Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules J. Chem. Theory Comput., 10, 2583-290, 2014]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Długosz, M.; Antosiewicz, J. Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments J. Chem. Theory Comput., 10, 481-491, 2014]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://browniandynamics.org BD_BOX Home Page]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*[http://browniandynamics.org BD_BOX Home Page]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td></tr>
</table>
Mdlugosz
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=14411&oldid=prev
Mdlugosz at 11:52, 21 October 2014
2014-10-21T11:52:55Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:52, 21 October 2014</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <del style="font-weight: bold; text-decoration: none;"><</del>ref<del style="font-weight: bold; text-decoration: none;">>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", Journal of Computational Chemistry '''32''' pp. 2734–2744 (2011)]</ref></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <ins style="font-weight: bold; text-decoration: none;">UNIQa0eb08b6ad1b2077-</ins>ref<ins style="font-weight: bold; text-decoration: none;">-00000006-QINU</ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms. BD_BOX uses <del style="font-weight: bold; text-decoration: none;">[[Flexible molecules |</del>flexible<del style="font-weight: bold; text-decoration: none;">]] </del>bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. <del style="font-weight: bold; text-decoration: none;">Non-bonded </del>potentials include pairwise functions describing screened <del style="font-weight: bold; text-decoration: none;">[[</del>electrostatics<del style="font-weight: bold; text-decoration: none;">]] </del>in dielectric media and <del style="font-weight: bold; text-decoration: none;">[[Lennard-Jones model |</del>Lennard-Jones functions<del style="font-weight: bold; text-decoration: none;">]]</del>. Hydrodynamically correlated motions of particles are <del style="font-weight: bold; text-decoration: none;">modelled </del>using configuration-dependent <del style="font-weight: bold; text-decoration: none;">[[</del>diffusion<del style="font-weight: bold; text-decoration: none;">]] </del>tensors. Brownian dynamics simulations can be performed either for single molecules or <del style="font-weight: bold; text-decoration: none;">[[Periodic boundary conditions |</del>periodic<del style="font-weight: bold; text-decoration: none;">]] </del>multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. <ins style="font-weight: bold; text-decoration: none;">Nonbonded </ins>potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are <ins style="font-weight: bold; text-decoration: none;">modeled </ins>using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Work on BD_BOX is supported by Polish National Science Centre.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Work on BD_BOX is supported by Polish National Science Centre.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><</del>references<del style="font-weight: bold; text-decoration: none;">/></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">UNIQa0eb08b6ad1b2077-</ins>references<ins style="font-weight: bold; text-decoration: none;">-00000007-QINU</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[http://<del style="font-weight: bold; text-decoration: none;">bionano</del>.<del style="font-weight: bold; text-decoration: none;">icm.edu.pl/software/bd_box </del>BD_BOX Home Page]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://<ins style="font-weight: bold; text-decoration: none;">browniandynamics</ins>.<ins style="font-weight: bold; text-decoration: none;">org </ins>BD_BOX Home Page]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td></tr>
</table>
Mdlugosz
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=11895&oldid=prev
Carl McBride: Added some internal links
2011-10-20T09:20:26Z
<p>Added some internal links</p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:20, 20 October 2011</td>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <del style="font-weight: bold; text-decoration: none;">program </del><ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", <del style="font-weight: bold; text-decoration: none;">J. Comput</del>. <del style="font-weight: bold; text-decoration: none;">Chem., 32:</del>2734–2744<del style="font-weight: bold; text-decoration: none;">, </del>2011</ref></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' <ins style="font-weight: bold; text-decoration: none;"> </ins><ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", <ins style="font-weight: bold; text-decoration: none;">Journal of Computational Chemistry '''32''' pp</ins>. 2734–2744 <ins style="font-weight: bold; text-decoration: none;">(</ins>2011<ins style="font-weight: bold; text-decoration: none;">)]</ins></ref></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>is an open source, scalable <ins style="font-weight: bold; text-decoration: none;">[[</ins>Brownian dynamics<ins style="font-weight: bold; text-decoration: none;">]] </ins>package for UNIX/LINUX platforms. BD_BOX uses <ins style="font-weight: bold; text-decoration: none;">[[Flexible molecules |</ins>flexible<ins style="font-weight: bold; text-decoration: none;">]] </ins>bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. <ins style="font-weight: bold; text-decoration: none;">Non-bonded </ins>potentials include pairwise functions describing screened <ins style="font-weight: bold; text-decoration: none;">[[</ins>electrostatics<ins style="font-weight: bold; text-decoration: none;">]] </ins>in dielectric media and <ins style="font-weight: bold; text-decoration: none;">[[Lennard-Jones model |</ins>Lennard-Jones functions<ins style="font-weight: bold; text-decoration: none;">]]</ins>. Hydrodynamically correlated motions of particles are <ins style="font-weight: bold; text-decoration: none;">modelled </ins>using configuration-dependent <ins style="font-weight: bold; text-decoration: none;">[[</ins>diffusion<ins style="font-weight: bold; text-decoration: none;">]] </ins>tensors. Brownian dynamics simulations can be performed either for single molecules or <ins style="font-weight: bold; text-decoration: none;">[[Periodic boundary conditions |</ins>periodic<ins style="font-weight: bold; text-decoration: none;">]] </ins>multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">BD_BOX </del>is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. <del style="font-weight: bold; text-decoration: none;">Nonbonded </del>potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are <del style="font-weight: bold; text-decoration: none;">modeled </del>using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Work on BD_BOX is supported by Polish National Science Centre.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Work on BD_BOX is supported by Polish National Science Centre.</div></td></tr>
</table>
Carl McBride
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=11888&oldid=prev
Mdlugosz at 15:58, 19 October 2011
2011-10-19T15:58:26Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:58, 19 October 2011</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><references/></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><references/></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==External links==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*[<del style="font-weight: bold; text-decoration: none;">http://</del>http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*[http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category: Materials modelling and computer simulation codes]]</div></td></tr>
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Mdlugosz
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=11887&oldid=prev
Mdlugosz at 15:57, 19 October 2011
2011-10-19T15:57:00Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 16:57, 19 October 2011</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011</ref></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011</ref></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Work on BD_BOX is supported by Polish National Science Centre.</ins></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
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</table>
Mdlugosz
http://www.sklogwiki.org/SklogWiki/index.php?title=BD_BOX&diff=11886&oldid=prev
Mdlugosz: Created page with "'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. ..."
2011-10-19T15:56:15Z
<p>Created page with "'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. ..."</p>
<p><b>New page</b></p><div>'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011</ref><br />
==References==<br />
<references/><br />
==External links==<br />
*[http://http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page]<br />
<br />
[[Category: Materials modelling and computer simulation codes]]</div>
Mdlugosz