[gmx-users] fixing protein during energy minimization
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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