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

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Wed Jul 23 14:53:47 CEST 2008

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 
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,

Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

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