[gmx-users] VMD Visulazation

[Victor Ma]

hello Gromacs community,

I have a quite embarrassing question to ask. I couldn't find a way to
visualize my gromacs trajectory in VMD. There are no tutorial online. By
nature, VMD does not recognize Gromacs toplogy file. I see that on
Gromacs's website there are two scrippts available: coarse_grain.tcl
<http://www.gromacs.org/@api/deki/files/89/=coarse_grain.tcl> and top2psf.pl.
For coarse_grain.tcl, I am not sure how to use it. I load it in the TCL
console, and nothing happens (no output, no error message). I type in the
command ./coarse_grain in both vmd window and tcl console and it just says
"invalid command". For the top2psf.pl script, I tried "./top2psf.pl -i
topol.top -o topol.psf". It says "Cannot open atoms for reading: No such
file or directory". But topol.top is my actual topology file. Please see
below:

; Include forcefield parameters
#include "charmm36.itp"
#include "PROA.itp"
#include "POPC.itp"
#include "TIP3.itp"
#include "SOD.itp"
#include "CLA.itp"

[ system ]
; Name
Title

[ molecules ]
; Compound    #mols
PROA               1
POPC             140
TIP3            8400
SOD              19
CLA              24


So can anyone please do me a huge favor to provide some instruction on how
to visualize my gromacs trajectory in VMD or where to find such
information.

Thank you so much.


Victor