[gmx-users] comparing simulations with diffrent forcefields

[Justin A. Lemkul]

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

-- 
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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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