[gmx-users] RMSD with Vsite vs No Vsites

Sikandar Mashayak symashayak at gmail.com
Thu May 5 18:21:54 CEST 2011


As a test case, I did two simulations one the usual Protein in Water and
other with Vsites at COM of each monomer but these Vsites dont interact with
anyone else. I was expecting results of these two should match almost
exactly, but when I compare the rmsd for Protein there seems to be

I once again checked my Vsites definitions and set up, there doesnt seem to
be any error in definition as per my understanding.

Is there any other reason that may be causing the mismatch? Or I may have
done something wrong in the setting up Vsites simulations.

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