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

[bharat gupta]

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 ..

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 ...

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

On Tue, Feb 22, 2011 at 6:31 PM, Justin A. Lemkul <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>
>>
>>
> --
> ========================================
>
> 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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-- 
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
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