[gmx-users] RMSD with Vsite vs No Vsites

[Sikandar Mashayak]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110505/40bb1deb/attachment.html>