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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


External links[edit]