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

neeru sharma neeru.bioinfo at gmail.com
Tue May 15 14:22:16 CEST 2012

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

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

Can anyone help me regarding the problems I am facing with the
visualization? Any help will be highly appreciated.

Thanks in advance


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