[gmx-users] equilibrium for box of simulation

[mohammad agha]

Dear Justin,

Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural, yes?
The cause of my doubt was because of in the most of articles was said for example " we select box with dimensions 10nm that after equilibrium was converted to 11nm" and I didn't see the report of decreasing of box dimensions! May I know your idea about it, Please?

Best Regards
Sara 




----- 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>
Cc: 
Sent: Thursday, October 4, 2012 7:57 PM
Subject: Re: [gmx-users] equilibrium for box of simulation



On 10/4/12 12:25 PM, mohammad agha wrote:
> 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?
>

You already have the density value; you posted it before.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
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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