[gmx-users] Re: High density after NPT

Justin Lemkul jalemkul at vt.edu
Fri Dec 21 01:15:36 CET 2012

On 12/20/12 2:47 PM, zugunder wrote:
> Could it be, say, because of still big conformational changes of the protein?
> The size of the system is not that small: the protein is hydrated with 10921
> water molecules.

Generally restraints are applied to the solute during equilibration to avoid 
structural changes due to clashes with solvent.  Pressure and density are 
related to box size, so any large change in the protein's conformation would 
probably be very obvious and potentially spurious.

> What are the variations of pressure and density that could be tolerated at
> this step?

Depends on the algorithm.  Pressure is a fickle metric (see 
http://www.gromacs.org/Documentation/Terminology/Pressure and previous 
discussions on this list).  It is generally advisable to run equilibration using 
weak coupling (i.e. Berendsen) methods, then switch to a more robust thermostat 
and barostat for further equilibration and data collection.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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