[gmx-users] fixing protein during energy minimization

Vaibhav Saraf saraf.vaib at gmail.com
Tue Feb 6 05:56:40 CET 2007

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.

> Vaibhav Saraf wrote:
> > Hi all,
> >
> > Can we fix the protein along with its water of crystallization, while
> > doing energy minimization with some additional water molecules? if
> > yes, how?
> Yes, they're called "position restraints". If you're serious about doing
> MD in GROMACS, please read about the first five chapters of the manual
> first. It's quite good, and reading it will help you avoid making silly
> mistakes, and avoid you not being aware of clearly-stated functionality.
> Mark

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