[gmx-users] Re: Some questions about genbox and EM (Tsjerk Wassenaar)

Erik Marklund erikm at xray.bmc.uu.se
Tue Jan 2 15:12:06 CET 2007

2 jan 2007 kl. 15.05 skrev Hu Zhongqiao:

> Thanks, Tsjerk
> > >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).
> I am running MD simulation in some protein crystals. I always find  
> that the water density in some big pore within protein crystals is  
> ca. 950 or even 920 kg/m^3 at 300K and SPC model, obvioulsy less  
> than 1000 kg/m^3 (bulk density). I think it will be more reasonable  
> if water density is closer to bulk density, right?

SPC bulk density is in fact less than 1000 kg/m^3, more like 970 kg/ 
m^3 i think. Your pore is still less dense than that, but not as far  
off as you thought.

/Erik Marklund

> >> 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.
> You are right in this point. I totally agree with you.
> >>
> > >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.
> I wonder if the structure of the system under the study is changed  
> during EM. For example, in my system consisting protein molecules,  
> water and counterion, some bond lengths in protein molecules will  
> be changed if I do EM without bond-lenght constraint. In this case,  
> some changed bond lengths in EM will be kept constant in  
> equilibration and production MDs because I use bond-length  
> constraint. I doubt its validaty. So I am thinking if it is more  
> reasonable to carry out EM with bond-length constraint.
> >
> >>Any comments are welcome.
> >I hope this helps.
> Cheers,
> Tsjerk
> 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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