[gmx-users] about NPT run

[Berk Hess]

Hi,

For position restraints there is an mdp option refcoord_scaling that sets how
the reference positions are affected by pressure scaling.

Berk

> 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.
> 
> -Justin
> 
> >     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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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