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?
Mark
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