[gmx-users] NVT NPT restrains

Ahmed Mashaly mashaly_1988 at yahoo.com
Tue Feb 20 22:57:31 CET 2018

Hi Justin
I see the point of restraining heavy atoms in NPT.The problem is that; no posre are included in the top file generated by Acpype, any suggestion to overcome that? Kind Regards,Ahmed

      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Tuesday, February 20, 2018 7:55 PM
 Subject: Re: [gmx-users] NVT NPT restrains

On 2/20/18 1:47 PM, Ahmed Mashaly wrote:
> Hi
> About the restrains, I see that it is necessary for NVT and NPT.
> For the .top and .gro produced by Acpype,
> https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM
> I don't have porse.itp nor anything related to restrain in the .top file, only for water
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j  funct  length  force.c.
> 1  2  1  0.09572  462750.4 0.09572  462750.4
> 1  3  1  0.09572  462750.4 0.09572  462750.4
> So what shall I do in this case? and what is the ideal time for NVT and NPT

Restraints are typically applied to solute heavy atoms to prevent 
distortion from initial, artificial configurations. It is very rare to 
need to restrain water, as that defeats the purpose of equilibration, 
which is primarily to allow the solvent to relax and achieve the desired 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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