[gmx-users] Re: Can i construct a solid wall in gromacs?

rajat desikan rajatdesikan at gmail.com
Tue Dec 4 07:20:15 CET 2012

I once constructed a solid hydrophilic wall by applying large constraints
on an equilibrated slab of spce water. Just construct a simulation box of
the size of the wall needed (don't make it too thin), equilibrate it, use
genrestr in all 3 dimensions to construct a restraints file, and then
genconf to place it in the final simulation box (after matching box sizes,
etc). It worked pretty well for me.

On Tue, Dec 4, 2012 at 3:31 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> > Dear All users
> >
> > Can i construct a solid wall in gromacs?
> >
> > --
> > Sincerely
> >
> > Ali Alizadeh
> Yes, you can. Atom-by-atom, until your castle is ready.
> If you start with 1-atom unit cell, you can then
> genconf -f unitcell.gro -o wall.gro -nbox $many $many $many
> Afterwards, the only challenge is to place this wall correctly into
> your [final] box.
> Dr. Vitaly V. Chaban
> MEMPHYS - Center for Biomembrane Physics
> Department of Physics, Chemistry and Pharmacy
> University of Southern Denmark
> Campusvej 55, 5230 Odense M, Denmark
> --
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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