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| '''VMD''' <ref>[http://dx.doi.org/10.1016/0263-7855(96)00018-5 William Humphrey, Andrew Dalke and Klaus Schulten "VMD: Visual molecular dynamics", Journal of Molecular Graphics '''14''' pp. 33-38 (1996)]</ref> is a molecular visualization program for displaying, animating, and analysing large [[Biological systems |biomolecular systems]] using 3-D graphics and built-in scripting. In addition to this VMD has a large array of extensions (see link below).
| | [http://www.ks.uiuc.edu/Research/vmd/ A molecular visualization program] for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. |
| ==Visualising a GROMACS trajectory==
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| Visualising a [[GROMACS]] trajectory:
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| first we produce a trajout.xtc file from the traj.xtc file, at the same time removing the [[periodic boundary conditions]]
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| :<code> trjconv -pbc whole </code>
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| then we load trajout.xtc into VMD:
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| :<code> vmd conf.g96 trajout.xtc </code>
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| ==References==
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| <references/>
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| ==External links==
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| *[http://www.ks.uiuc.edu/Research/vmd/ VMD web site]
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| *[http://ftp.ks.uiuc.edu/Research/vmd/plugins/ VMD extensions page]
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| *[http://www.nvidia.com/object/vmd_on_tesla.html VMD on Tesla GPUs]
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| [[Category: Materials modelling and computer simulation codes]]
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