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

[Mark Abraham]

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 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. 
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.

Mark