Re: frozen water Oxygens

From: Chris Harrison (
Date: Wed Aug 05 2009 - 09:01:24 CDT

I'm assuming you're using TIP3P waters .... per the original Jorgensen paper
the H's of TIP3P are fixed .... ie, in the TIP3P model they are not designed
to move except through rotations or translations of molecular water. This
is one reason the command
"rigidbonds water" exists. Further, since hydrogen atoms may behave quantum
mechanically at room temperature, which MD by itself cannot model, it's not
clear if you are trying to model something or just trying to minimize the
hydrogen positions of your system .... can you clarify?


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733 <>
Fax: 217-244-6078
On Tue, Aug 4, 2009 at 11:13 AM, Mark M Huntress <> wrote:
> Hi,
>       I am trying to run an MD simulation where only the H's of the waters
> of my solvent box are free to move. I have just completed an MD where the
> entire water molecules were free tomove, and it seemed to work fine, but now
> that I have frozen the Oxygens, the simulation becomes unstable, and the
> velocities of the H's exceed 10,000. It does not help to start the
> simulation from a lower temperature either, that just makes the H's go
> faster, 1.2e+24 for example. Using harmonic constraints does not seem to be
> helping much either.  Any suggestions?
> Thanks,
> Mark

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