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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). | '''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). | ||
==Visualising a GROMACS trajectory== | |||
Visualising a [[GROMACS]] trajectory: | |||
first we produce a trajout.xtc file from the traj.xtc file, at the same time removing the [[periodic boundary conditions]] | |||
:<code> trjconv -pbc whole </code> | |||
then we load trajout.xtc into VMD: | |||
:<code> vmd conf.g96 trajout.xtc </code> | |||
==References== | ==References== | ||
<references/> | <references/> | ||
Latest revision as of 12:35, 2 April 2014
VMD [1] is a molecular visualization program for displaying, animating, and analysing large biomolecular systems using 3-D graphics and built-in scripting. In addition to this VMD has a large array of extensions (see link below).
Visualising a GROMACS trajectory[edit]
Visualising a GROMACS trajectory:
first we produce a trajout.xtc file from the traj.xtc file, at the same time removing the periodic boundary conditions
trjconv -pbc whole
then we load trajout.xtc into VMD:
vmd conf.g96 trajout.xtc