[gmx-users] fudge QQ values

[Justin A. Lemkul]

Yun Shi wrote:
> Hello everyone,
> 
> I just have a quick question. So the fudgeQQ value for amber99sb force 
> field in gromacs is 0.8333, but I wonder if we should use 0.833333 or 
> 0.83333333?
> 
> I quite different simulation results by manipulating this value. In my 
> antibody - ligand system, 0.8333 showed ligand not stable, dropping out 
> of the binding site, while 0.83333333 showed the same ligand fairly 
> stable. The trajectories are about 50 ns long.
> 

FudgeQQ values are applied to intramolecular 1-4 electrostatic interactions. 
The value has no bearing on the intermolecular interactions between your protein 
and ligand.  So unless your ligand's structure became completely spastic such 
that it pushed itself out of the active site, I doubt the value has any effect, 
especially with a difference of 0.004% between the FudgeQQ values.

Also realize that the fact that one trajectory did one thing, and another 
behaved differently, is not necessarily indicative of the problem.  Now if you 
have several simulations under each condition that all behave in the same way, 
you may have some reason for concern.  It could just be that the one simulation 
run with 0.8333 for FudgeQQ behaved anomalously, and if you ran it 10 more times 
(with different starting velocities), it would be stable.

-Justin

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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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