[gmx-users] Re: solvation
tsjerkw at gmail.com
Fri Aug 14 08:05:19 CEST 2009
Right, but genbox puts things inside the rectangular brick
corresponding to the unit cell, starting at the origin. That means
that if the solute is on one end, then placing something close to the
part that sticks out will actually be put on the other side of the
box. But maybe I just want to make it too simple :)
On Thu, Aug 13, 2009 at 11:25 PM, Vitaly V. Chaban<vvchaban at gmail.com> wrote:
> I understood the situation in such a way that MD was not run at all,
> so Jamie visualizes *gro* file obtained with *genbox*...
> didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/
> to prepare your system?
>>> Thanks for the answer. When I said far away means my pore was in one corner
>>> of vmd window and the water molecules in opposite corner (almost).
>> Did I miss something or did neither Vitaly nor Justin reply "Are you
>> perhaps seeing the effect of periodic boundary conditions?".
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
More information about the gromacs.org_gmx-users