[gmx-users] image jumps in VMD

David spoel at xray.bmc.uu.se
Mon Jun 24 13:07:13 CEST 2002

On Mon, 2002-06-24 at 12:07, Dr. Y. U. Sasidhar wrote:
> I use vmd_1.72 to visualize gromacs md trajectory using "animate".
> 1. Frequently the image jumps between edges and goes out of visible
> screen window.
> How do I avoid this ? ( centering in a frame also does not work ).
> How can I have image always in field of view so that I can view
> trajectory completely without "interruptions".
This is due to periodic boundary conditions. The only real solution is
to fit the trajectory to the starting structure:
trjconv -s topol.tpr -f traj.xtc -o traj-fit.xtc -fit

> 2. Can I save pdb file of a particular frame number in VMD ?
Probably, but you can do it with trjconv anyway:
trjconv -s topol.tpr -f traj.xtc -o conf-time.pdb -dump time
(where you replace time by the timepoint you want to dump)

> Sasidhar
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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