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

[Justin A. Lemkul]

bharat gupta wrote:
> Since the paper that I am following says that for that protein (GFP) 1ns 
> simulation is enough as other people carried out 10ns for the same 
> protein and rmsd follows the same pattern which is being shown by that 
> 1ns simulation ..

When were those studies published?  With modern hardware and a recent Gromacs 
version, you can get 10 ns is two days' time, and the data you collect 
represents a time scale well below most biologically-relevant events except the 
smallest of motions.  A paper that did only 1 ns should be fairly old, I imagine.

> 
> So I decided to do a 3ns simulation .... the RMSD that I got was same as 
> that mentioned in the paper ... showing that the barrel doesnot show 
> much fluctuation and remains stable for a 3ns simulation (similar to 
> that 1ns one).
> 
> Again I decided to go for 10 ns simulation this time but I changed the 
> force field this time ... I got a different trajectory ...
> 

All trajectories (theoretically, if starting from independent velocities) are 
"different."  You can't expect everything to be identical, especially over short 
time periods.  Multiple replicates over long time frames should converge to some 
meaningful averages of the observables of interest.  Time averages would equal 
ensemble averages once the initial "memory" of the system is lost.  This is 
ergodicity.

> What shall I do now ?? .. shall I repeat that 10ns simulation with the 
> same FF that I was using for 3ns simulation ?? 
> 

You should do your homework about which force field model you believe should be 
most accurate, basing your choice on (1) papers that have studied the same or 
similar systems and (2) systematic comparisons of force fields to understand 
their inherent limitations and benefits.  There are several such papers that 
have come out in recent years, some more complete than others.  The results of 
(2) should supersede the results of (1): if a group used force field X on system 
Y, but then force field X was later shown to incorrectly reproduce some 
important aspect of system Y, then force field X is probably a bad choice, even 
if there is some element of precedent.

-Justin

> On Tue, Feb 22, 2011 at 6:31 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
>         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
>         Mobile no. - 010-5818-3680
>         E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>         <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> -- 
> 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
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
> 

-- 
========================================

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

========================================