[gmx-users] about equilibrium
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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