[gmx-users] about equilibrium

mohammad agha mra_bu at yahoo.com
Mon Oct 15 18:11:47 CEST 2012

Dear Justin,

Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject "equilibrium for box of simulation". When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct?

Best Regards

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: Monday, October 15, 2012 5:21 PM
Subject: Re: [gmx-users] about equilibrium

On 10/15/12 8:56 AM, mohammad agha wrote:
> Dear Gromacs Users,
> I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent and additives (that before I had equilibrated them separable) in the box of surfactant (by genbox) and equilibrated it totally.
> May I know that this work is correct or not, Please?

Maybe.  It's hard to tell.  Note that when you post the same thing four times and do not get a reply, it's usually due to the fact that it's hard for us to figure out what's going on.

I don't know what your goal is but your approach is a bit hard to comprehend as written.  One can usually build a multi-component system rather easily with a few invocations of genbox -ci -nmol, but then too, I don't know if you need some particular configuration (surfactant micelles?) or if random positions will suffice.  Prior equilibration of solvent is probably a good approach.


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

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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