[gmx-users] On initialization of the molecules

Bao Kai paeanball at gmail.com
Sat Apr 13 20:31:49 CEST 2013

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.

Thank you very much.

Best Regards,

More information about the gromacs.org_gmx-users mailing list