[gmx-users] Some questions about genbox and EM

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Tue Jan 2 14:05:58 CET 2007

Dear all,
Now I have 3 questions.
1) Do I need to use genbox to add H2O twice?
In the past, I first used genbox to add H2O and then used genion to add
counterion. After that is EM. But now I find, if I use genbox again
after genion or even after EM, there are some additional, though very
few, H2O molecules will be added into system. So I want to ask if the
method to use genbox twice is more reasonable?
2)One or two EM?
Some users mention that one EM will be done after adding H2O and the
second will be done after adding counterion. In the past, I just did one
EM only after adding counterion. Is it more reasonable to do one EM
right after adding H2O?
3) bond-length constraint in EM or not?
In the past, I did EM without bond-length constraint. But lately one
person, who is obviously more expericed in MD than me, told me that I
should do 2 EM, 1st with bond-length constraint and 2nd without it. Is
it more reasonable?
Any comments are welcome.
Zhongqiao Hu
Lab E5-04-27
Tel: 65161946(O)
Department of Chemical and Biomolecular Engineering
National University of Singapore
117576, Singapore
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