[gmx-users] On initialization of the molecules

Justin Lemkul jalemkul at vt.edu
Sat Apr 13 20:33:26 CEST 2013

On 4/13/13 2:31 PM, Bao Kai wrote:
> Dear Gromacs Team and users,
> I have been using Gromacs for one of my projects before. For that project,
> I initialized the molecules in a random way. I mean, I used genbox to put
> the solute molecules (much fewer) first, then used genbox to put the
> solvent molecules (much more).
> Now, I want to simulate the interface for the mixtures with different
> molecules. For the initialization, I want to put one kind of molecules in
> one side while put the other kind of molecules in the other side. If I
>   initialize the molecules in a random way, I think I may get a lot of
> droplets, which is not very desirable.
> I wonder if you could please tell me how to do the initialization in this
> way with Gromacs.




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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