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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 2 15:38:56 CET 2007

Hi Zhongqiao Hu,

You didn't mention that your system consisted of protein crystals.
Maybe I shouldn't have just assumed that it was about proteins in
solution, but still...

> 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?

With protein crystals, it becomes a bit of a different matter. In the
cavities, you may not actually have "bulk" densities, since the
protein environment may have long range ordering effects. Ordering
effects potentially reach up to a nanometer, so only in the central
regions of large cavities do you expect bulk density. For all cavity
volume the density is likely to be less. In addition, as Erik pointed
out, SPC bulk density is already lower. You should probably find some
reference of how much water there should be in your protein crystal.

> 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.

When doing EM without constraints, you allow optimization of the bond
lengths in the system. Then doing EM with bond constraints doesn't add
anything, you're bond lengths are constraint, just as they will be
during equilibration and production MD. You might just as well skip EM
with bond constraints. If you're structure is not reasonable enough
for MD after EM without constraints, it is unlikely to be so after EM
with constraints.

> >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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