[gmx-users] VMD Visulazation

[Justin Lemkul]

On 6/1/15 12:07 PM, Victor Ma wrote:
> 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.
>

Load the starting coordinate file, then load the trajectory as data for that 
molecule.  The topology is never involved.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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