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
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