[gmx-users] equilibrium for box of simulation

mohammad agha mra_bu at yahoo.com
Thu Oct 4 18:25:26 CEST 2012

Dear Justin,

Thank you very much from your help.

Oh, yes, the vectors of box are downward in the first with much slope and then the slope became milder and milder and then it become almost fix.

For checking of density, should I use from formula: d=m/v?

Best Regards

----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, October 4, 2012 7:01 PM
Subject: Re: equilibrium for box of simulation

Please keep the discussion on the gmx-users list.

On 10/4/12 11:28 AM, mohammad agha wrote:
> Dear Justin,
> Thank you very much from your help.
> I don't know about "vectors trending downward, or do they converge"

You can plot box vectors from the .edr file.  That will give you their values and show trends in the data.

> The change of density is from 1274 to 1685. and the slope of increasing the density at the first is much and then it become almost fix.

This outcome suggests that your box likely has stabilized.  You should still plot the vectors to understand what's going on.  You also need to assess whether or not this density is acceptable as an evaluation of your physical model of the system.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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