[gmx-users] using VMD with GROMACS trajectories

Mark Abraham 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.
> Mark

This is classic Wiki material... how are we going with this?


More information about the gromacs.org_gmx-users mailing list