[gmx-users] about equilibrium

Justin Lemkul jalemkul at vt.edu
Mon Oct 15 15:51:45 CEST 2012

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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