[gmx-users] Pressure and box volume

Mishelle Oña samimishu at hotmail.com
Mon Mar 20 16:55:14 CET 2017

Hello Justin,

Thanks for your response. I made the following steps before the pressure error happened:

1)Built a system of 1 polymer (30 monomer)

2)Run EM simulation in vaccum

3) Add solvent (water)

4) Run a EM simulation with the solvated system

5) Run a relaxation simulation

6) Run a NVT simulation

7) Run NPT simulation (when the problem occured)

It is supposed that NVT simulation stabilizes temperature and it actually does. Then NPT simulation is used to stabilize the pressure but this did not happend. I run a 500 ps and the a 5000 ps simulation and it still has the same pressure of 300 bar aprox.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Monday, March 20, 2017 6:54 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Pressure and box volume

On 3/19/17 8:42 PM, Mishelle Oña wrote:
> Hello Justin!
> I was trying to getting down the pressure of my simulation from aprox 300 bar to 1 bar. I increased the box volume and now I have 27 bars but my density decrease dramatically from 970 to 320 kg/m3. I tried to add more water molecules to increase it again but then the pressure scaled up to 300 bar again. To make a production simulation we should equilibrate the parameters of Temperature, Pressure, density and Volume. Should I continue playing with the size of the box and the amount of water molecules until I get all this parameters acording to the conditions I want or is anything else I can do instead?

"Randomly toying with box size and water content" is not a reproducible method :)

We're missing a lot of context here, like everything you've done up to this
point, so it's really hard to comment.  But in general, it is certainly not
necessary to make all these ad hoc changes.  You may just have to wait a while
for the pressure to stabilize, depending on how far from equilibrium your
initial state was (and it sounds like it was pretty far from your desired value).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above.

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