[gmx-users] Position restraints

[Justin Lemkul]

On 4/2/13 6:07 AM, alex rayevsky wrote:
> Dear All!
> I have a doubt about the rightness of ligand/molecule integration in the
> topology file. I'm using an amber (tleap) or swissparam.ch to build a
> topology of the residue (modified trna). Is it neccessary to generate a
> position restrain file (genrestr program) for this residue or not? I've
> started both dynamics with/without posrestraints on my residue, however I'm
> really not sure that my results from both of them are different. But I want
> to do everything in right way, so what can you say about this?
>

Restraints during equilibration are used to prevent unnatural forces from the 
unequilibrated solvent and help prevent deformation of the structure.  It's 
never a bad idea to restrain the whole solute.  If I were reading a paper that 
described restraining the whole solute, except for one residue because it was 
special or difficult to deal with, I would immediately be suspicious.

-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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