[gmx-users] Re: solvation

[Tsjerk Wassenaar]

Hi,

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 :)

Cheers,

Tsjerk

On Thu, Aug 13, 2009 at 11:25 PM, Vitaly V. Chaban<vvchaban at gmail.com> wrote:
> Tsjerk,
>
> I understood the situation in such a way that MD was not run at all,
> so Jamie visualizes *gro* file obtained with *genbox*...
>
> Jamie,
> didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/
> to prepare your system?
>
>
> Vitaly
>
>
>>
>>> 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
>>
>> --
>> 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
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623