[gmx-users] using VMD with GROMACS trajectories
Mark.Abraham at anu.edu.au
Wed May 16 10:51:57 CEST 2007
Mark Abraham wrote:
> Roughly speaking, a gromacs .top file has the same sort of information
> as a .psf file, but VMD won't read one natively. Instead, give VMD a
> structure file (.gro, .g96, .pdb or anything else) that corresponds (in
> the same order) to the atoms that are saved in your trajectory in place
> of the .psf file, and then load the trajectory (.trr or .xtc) into that
> molecule in the same way you would a .dcd file (see the VMD manual if
> you don't understand this step). VMD will guess the atom connectivity
> based on the original structure you give it - you should not expect this
> connectivity to correspond perfectly to that in your .top file.
> The gromacs tool ngmx can do a rough and ready visualization, if the
> right X libraries exist and ngmx was installed. See "man ngmx" for info.
This is classic Wiki material... how are we going with this?
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