Hi 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 discrepancy.
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. thanks sikandar
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