VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 06 2015 - 10:24:36 CDT

Hi,
  If I understand your description correctly, you've run a GROMACS
simulation with an incorrect periodic unit cell, and you want to
correct the way it is displayed in VMD? The VMD atom selection commands
allow the periodic cell dimensions to be set to arbitrary values after
a trajectory is loaded, so in principle it is likely possible for you to
use the pbctools plugin to unwrap the trajectory and then rewrap with a
different unit cell size, but this seems somewhat problematic.
It would be helpful if you made a small JPEG image of what you see now
and explain what you're hoping to get ultimately.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 05, 2015 at 08:58:31AM +0000, Ming Tang wrote:
> Dear all,
>
>
>
> I did a simulation using periodic boundary conditions pbc=xyz in GROMACS.
> It turns out that the box is defined too small, and some atoms go to
> another box.
>
> how to display the real model (without separation) in VMD?
>
>
>
> Thanks in advance,
>
> Ming 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/