[gmx-users] Re: solvation

Vitaly V. Chaban vvchaban at gmail.com
Thu Aug 13 23:25:34 CEST 2009


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
> --
> 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

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