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

[Justin A. Lemkul]

bharat gupta wrote:
> 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 ??
> 

Different force fields can give different results, unfortunately.  There are 
several comparisons in the literature among common force fields.  Understanding 
inherent limitations and assumptions in each model is an important (read: 
absolutely critical) part of designing a simulation.

Also realize that you're comparing an extremely short (3 ns) trajectory with a 
moderately short (10 ns) one.  In theory, exhaustive sampling (i.e. orders of 
magnitude larger than what you've done) should converge over all simulations. 
But due to the inherent differences in parameter sets, this is unlikely to be 
the case.  The fact that your simulations are so short probably magnifies this 
effect.

-Justin

> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
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> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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