[MMTK] solvation of protein molecule

prabhakar g prabha.iisc at googlemail.com
Fri Jun 4 01:25:40 UTC 2010


Dear All,

I tried to solvate a protein molecule using the solvation.py, and am getting
two output files corresponding to solvation and equilibration. When i try to
visualize the file equilibration.nc with the VMD, i am getting images of
distorted water molecules ( probably the bond lengths in them). I am
attaching the image of one of the distorted snapshot and the script for you
reference, why does this happen, is there anyway to correct it, hope
somebody can help. Thanks

Sincerely
prabha
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