[gmx-users] Some questions about genbox and EM

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 2 14:42:51 CET 2007

Hi Zhongqiao Hu,

> 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?
Assuming that you mean placement inside a protein, I don't think it is
necessary. For the solvent itself or the interface, it really doesn't
matter. During EM, or even during MD, some cavities may be generated
which could be filled with a water molecule, but that doesn't mean
they should be occupied. Of course, it would be interesting to test
whether your results improve, i.e. one or the other leads to a more
stable system. In that case, you should also try the placement of
water by optimization of the orientation (which isn't done using
genbox and is much more costly).

> 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?
It's not likely to be necessary. EM (prior to MD) is just to obtain a
reasonable structure which can be used to start an MD run with,
without exploding due to bad contacts/strained geometries.

> 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?
Again, not necessary, see point 2.

> Any comments are welcome.
I hope this helps.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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