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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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