[gmx-users] Re: Differences in rmsd with different force field

bharat gupta bharat.85.monu at gmail.com
Wed Feb 23 03:27:10 CET 2011


I did a simulation of 3 ns with OPLS AA 2001 Force Field for a protein of
230 aa and also I carried out a simulation of 10ns for the same protein but
with different force field (Amber 2006) . I obtained the rmsd of the
trajectories of both simulation , which I found to be different ?? i.e. 3ns
rmsd from one simulation doesnot superimpose with another (10ns) .. why
there is such a difference ??

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