[gmx-users] Problem in visualizing protein-ion complex trajectory in vmd

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 15 14:29:24 CEST 2012

On 15/05/2012 10:22 PM, neeru sharma wrote:
> Dear gromacs users,
> I am running steered MD simulation using Plumed plugin in gromacs for 
> a system consisting of Protein-Mg-GTP complex. I have to calculate the 
> distance of specific atoms with Mg and GTP.
> While visualizing the trajectories using vmd, I am encountering some 
> problems.
> 1) While using the "-pbc" flag with "whole" option, the protein is 
> visualized properly, but the Mg and GTP are showing jumps moving away 
> from the protein structure. That is why, the distance between Mg, GTP 
> with atoms of the protein is not coming out properly.
> 2) While using the "-pbc" flag with "nojump" option, the protein is 
> visible in stretched and distorted geometry, but the Mg and GTP are 
> intact with the structure. Here, the distance between Mg,GTP with 
> atoms of the protein is calculated correctly.
> 3) Then, I tried with both the whole and nojump options,used in 
> succession (first whole and then nojump), but still the protein is not 
> visualized properly. It is visible in stretched geometry only, as was 
> visible with nojump.
> Can anyone help me regarding the problems I am facing with the 
> visualization? Any help will be highly appreciated.

See suggestions here 
You will perhaps need to identify a frame where everything is in the 
box, and then choose a suitable (new?) group for the various operations, 
or do multiple passes with trjconv.


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