[gmx-users] image control

Alan Dodd anoddlad at yahoo.com
Tue Jan 15 16:13:15 CET 2008

I'd suggest this is an issue with VMD rather than gromacs.  You have to be quite careful which .gro you use to provide the original structure, make sure it is actually the starting frame and not anything else - this is something I've seen cause this sort of problem before.
Normally, of course, PBC settings in Gromacs keep molecules whole in the output file quite reliably, but not knowing how you've set your simulation up, I couldn't comment on that.  Using ngmx is a good way to check that Gromacs itself is doing what you think it is.

----- Original Message ----
From: Myunggi Yi <myunggi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, January 15, 2008 2:51:20 PM
Subject: [gmx-users] image control

Dear users,

I'm running NPT simulation POPC with a short peptide.
I see the long bonds across the unit cell in VMD.
Why am I getting broken lipid molecules in the trajectory (original .xtc file w/o any post-modification)? 

Some lipids move whole molecules, but some are broken.
How can I control the unit of image?
I couldn't find any related word in the manual.

I assume image will be done by "residue".
Then I shouldn't get this strange result. 

I got the popc.itp from Dr. Tieleman's web site.
Any idea?

Best wishes,

KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334

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