[gmx-users] Position restrained..

[Mark Abraham]

On 21/11/2010 4:01 AM, pawan raghav wrote:
> Dear All,
> Hope this mail will find you in good health.
>
> I am facing a problem regarding Position restrained dynamics (PR). I 
> have done Molecular dynamic simulation
> (for cytosolic protein) but has not performed PR. So i m little 
> confused if this effects the results and if yes to what extent it 
> effects the outcome,
>
> Earlier, i performed PR as it is recomended but in my cases ,the 
> generated structure was not correct as the core residues found to be
> reduced from 82%-52% and one bad contact was also observed. So i 
> skipped the PR Step and run MD
> simultaion just after energy Minimization.
>
> I was wondering if PR is always necessary before molecular simulation 
> without any exception. And if not, how can i justify this protocol
> that we have performed without PR. Or where i can find the references 
> to justify the my protocol.

The purpose of position-restrained equilibration is to inhibit the 
system from moving far from the starting configuration while it is 
equilibrating. How vital this is to your intended observation will drive 
whether you care much about doing it. If it does not succeed in 
preserving a structure, then either the restraints were not done 
correctly, or your system is intrinsically unstable.

Mark