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. Thanks in advance Regards, Neeru
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