From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Thu Feb 12 2004 - 16:16:40 CST
Does anyone know how to deal with constraint failures in the RATTLE
algorithm? I have been trying to heat up the solvent with ions for a
protein system that is fixed, temperature set to 1000. However, I have had
continuous problems with certain atoms shaking too much and the whole
system becoming unstable. I thought doing some minizations to equilibrate
the system on the fly would do the trick. However, it seems that there is
always one atom (not the same one, varies from simulation to simulation)
that destabilizes the system. Do I need more minizations?
I have checked that my system is well inside the bounding box.
Does anyone have any word of direction?
Computer Science Department,
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