[gmx-users] How to build boxes with constant number of solvent molecules?
Peyman.Yamin at cbi.uni-erlangen.de
Wed Jul 23 14:53:47 CEST 2008
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,
Lehrstuhl fuer Thermische Verfahrenstechnik
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de
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