[gmx-users] Re: solvation

Vitaly V. Chaban vvchaban at gmail.com
Thu Aug 13 18:21:17 CEST 2009


I didn't understand why you meant saying "waters far from the outside
of the pore"... Far from outside, then where exactly? Maybe I just
imagine your box incorrectly.

To fill the pore with a solvent try to "deceive" genbox a little:
1) make a box (see editconf) in such a way that it contains only
"inside" part of your pore. genbox will not report an error from its
2) add the solvent with genbox.
3) return to the original box size.
4) add the outside part.


> I want to know how can I use genbox to fill inside of the pore as well as a
> layer outside. From the "man genbox" page I try to use -shell with a
> negative value (?) but it put waters far from the outside of the pore and I
> think it does not care about the sign. It seems strange to me because when I
> had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a
> layer of few molecule around the pore, but when I change it to 1. 1. 1., the
> water molecules generated far away. I appreciate if someone tell me (1) how
> I can add water inside the pore and (2) why changing the box size will give
> a opposite result. Please advise..Thanks in advance/Jamie

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