[gmx-users] fixing protein during energy minimization

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 6 06:26:54 CET 2007

Vaibhav Saraf wrote:
> My system consists of the protein, water of crystallisation and
> additional water molecules. And before doing the position restraint
> MD, I wish to perform energy minimization once with the protein and
> its water of crystallisation fixed and only the additional water
> molecules free. Later would do it un-restrained.
> So need guidance on whether I can fix the protein (along with its
> water of crystallisation) during energy minimization.

Well this two-stage minimization sounds like something few people would 
bother doing, since everything will start moving once you get to doing 
MD after the EM, and this crystal structure you seem to be trying to 
preserve is only an approximation to the ensemble of structures in the 
crystal anyway. So people on this list could well not know (or care) 
whether such a technique is implemented.

In any case, it can't hurt to try the effect of position restraints in 
the EM, since you can readily tell whether the protein structure has 
been meaningfully perturbed. In fact, you can also do EM without the 
restraints and see what happens there too.

Also, if you'd gotten to page 15 of the 3.3 manual by now, you'd have 
found out about something else you could try.


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