[gmx-users] about NPT run
gmx3 at hotmail.com
Fri Sep 17 11:02:05 CEST 2010
For position restraints there is an mdp option refcoord_scaling that sets how
the reference positions are affected by pressure scaling.
> Date: Thu, 16 Sep 2010 21:15:38 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] about NPT run
> zhongjin wrote:
> > Hi,
> > I want to run a NPT run,could I put some groups into position
> > restraint, or make them frozened ?
> > I find it is OK in NVT ensemble. But I am not sure whether it is proper.
> Frozen groups cannot have their coordinates scaled by pressure coupling. I
> believe this can lead to spurious contributions to the virial and pressure, so
> it is generally recommended that NPT not be combined with frozen groups.
> > Thanks!
> > Zhongjin He
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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