[gmx-users] How to build boxes with constant number of solvent molecules?

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 23 16:20:02 CEST 2008

Peyman Yamin wrote:
> Hello dears,
> I want to solvate different conformations of a molecule in a water box and I 
> want to have the same number of solvent molecules in my box at the end. 
> I do it with genbox but end up with different number of solvent molecules. A 
> random insertion of more molecules results in a box which would not be easily 
> equilibrated.
> I also tried to solvate in a larger box and then delete some molecules from 
> the end of file so that I have a certain number of molecules for all of them, 
> but it also results in a strange looking environments in the box which mostly 
> lead to an equilibration crash.
> Does one know any practical strategy to solvate a molecule in a box and have 
> the number of solvent molecules fixed??
> I appreciate any suggestions,
> regards,
> Peyman
genbox -maxsol

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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