[gmx-users] Re: equilibrium for box of simulation

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 17:31:35 CEST 2012

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 



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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