From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Tue Aug 04 2009 - 11:13:12 CDT
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?
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