[gmx-users] regarding visualizing the output

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jun 13 09:28:30 CEST 2006

Hi Lali,

In VMD you can view .xtc files directly. Check the gromacs archive or the
VMD manual. Besides, you can use trjconv with -b and -e to extract a certain
time frame. Please check the Gromacs manual or try trjconv -h (also to find
out what else is possible).

Best regards,


On 6/13/06, lalitha selvam <hayagrivar at hotmail.com> wrote:
> hello sir,
> 1.i ran simulation for 2 ns.....i want to view the structure from 1500 to
> 2000 frames at every 25 ps.how to get it in pdb strucutres of the above
> wanted frames.
> 2.with the use of trjconv i had one pdb file converted from one frame. i'm
> viewing that structure with VMD, but when i'm trying to load in NOC
> software
> i'm not able to view.cant we view that pdb structures converted from
> gromacs
> in other visualization software.
> please anyone explain me.
> regards
> lali.s
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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