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

[bharat gupta]

Hi

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 ??

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
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E-mail : monu46010 at yahoo.com
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