hello
I have 200 ns simulation of a peptide and i want to calculate average structure of the simulation.
I used this command:
g_rmsf -f md.xtc -o rmsf.xvg -s md.tpr -ox av.pdb
The resulting pdb structure has a lot of clashes and it is not a good structure for further analysis such as docking procedure.
I minimized the structure but the problem is fixed and gromacs said the minimization could not reach to f max.
could any one help me?
An average structure is not necessarily anything physically meaningful.
http://www.gromacs.org/Documentation/Terminology/Average_Structure
You would be better off clustering the snapshots, and then use that information to identify a most representative structure from the dominant cluster.
An average structure is not necessarily anything physically meaningful.
http://www.gromacs.org/Documentation/Terminology/Average_Structure
You would be better off clustering the snapshots, and then use that information to identify a most representative structure from the dominant cluster.
To exemplify: imagine the average coordinates of a methyl group that is free to spin around the X-C bond. That would be a very unphysical structure and not be looking much like a methyl group.
Thank you Justin, I think your opinion is more reliable. I work according to your instruction.
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