Re: question regarding simulated annealing

From: Chris Harrison (
Date: Thu Aug 30 2012 - 02:28:00 CDT


Puspita Halder <> writes:
> The only problem that
> I found is the water density around the protein in the solvation box. This
> is found to be kind of inhomogeneous means in some portion of the box water
> is more dense whereas in the other portion it is less dense though the
> protein remains always solvated .

Are you trying to say you have a vacuum bubble(s) in your bulk solvent?

If not, do you have some quantitive way of clearly demonstrating the
difference in density between different regions of the box?

It is not uncommon in a non-equilibrium state for the density in a bulk
solvent to be inhomogenous throughout the box (ie you system has not
finished dissipating the energy from the higher temp state, or your
system is simply not equilibrated, etc); but your description at the
moment is a little too vague for much concrete help.

You might consider loading your system in VMD and writing a tcl script
where you box is subdivided into sub-cells and you calculate the
"density" or even just the number of water atoms for each sub-cell in
each frame of your 2ns dcd. Should only take you an afternoon or day to
do this, much less if you're familiar with tcl scripting and vmd. From
this you could graph the resulting values for each subcell as a function
of time and also calculate the average "density" for each sub-cell. The
relative difference between the resulting values of the sub-cells would
help everyone understand more clearly the potential problem you're
observing. At the moment, it's hard to tell concretely what is
happening in your bulk solvent, providing more precise info might help
us provide more concrete help..


Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078               Fax:   217-244-6078

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