[gmx-users] NVT Equilibration

Dallas Warren Dallas.Warren at monash.edu
Thu Oct 6 22:36:49 CEST 2011

Ravi, not entirely sure what you are actually doing / aiming to do, but another option is to run the system NPT, which means the box size will scale to give the correct pressure / density, then you take that and run your NVT run.  But that means you will end up with possibly a substantially smaller box, which may be an issue.  But, closer you are to the correct starting point when you build the box the better.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Thursday, 6 October 2011 9:35 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] NVT Equilibration
> Ravi Kumar Venkatraman wrote:
> > *Dear All,
> >               But I scaled the solvent box according to the density
> > using editconf_d command line. Then I carried out EM and NVT
> equilibration.*
> >
> Scaling the box with editconf simply scales the coordinates of the
> molecules in
> it, which may or may not produce a physically stable condition.
> Building a
> better starting box is the proper solution, as Dallas suggested.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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