[gmx-users] comparing simulations with diffrent forcefields

[Kowsar Bagherzadeh]

Dear Justin,
 
Thank you very much for the reply
 
Sogol


________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Kowsar Bagherzadeh <kw_bagherzadeh at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, May 28, 2012 6:06 PM
Subject: Re: [gmx-users] comparing simulations with diffrent forcefields



On 5/28/12 7:07 AM, Kowsar Bagherzadeh wrote:
> Dear users,
> I have done a Ligand-Protein Simulation using 43a1.ff forcefield and
> ssDNA-Protein (the same protein I used for ligand protein simulation) using
> amber99sd-ILDN forcefield. Is it possible to compare the results of the two
> simulation with eachother? No?

Maybe it's possible, but there will be a lot of caveats to the results.  You may know of some intrinsic limitations or benefits of each force field that may explain away discrepancies, but the real complication comes with the ligand. How did you generate its parameters?  Do you know exactly how those parameters will affect the local dynamics of the residues in which it makes contact?  Do you know the equivalent result using a suitable Amber force field?  If the answer to any of these questions is no, you'll have a hard time convincing a reviewer that your comparison is very meaningful.

Net result: choose a force field, and use it for all simulations you wish to compare.  It is substantially easier than trying to wiggle your way into a potentially incomplete or incorrect interpretation of the results.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
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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