From: Peter Bazeley (peter.bazeley_at_gmail.com)
Date: Mon Jan 03 2005 - 17:27:45 CST
I am simulating a protein with NAMD, using a basic set of parameters.
I minimize my protein for 1000 timesteps, then run for 50000
timesteps. I've found that the TOTAL energy of the system increases
over time. I guess I'm trying to figure out the reason behind this.
Could it be that I am seeing the entropic effects on the protein over
time? Or perhaps the minimization created a structure that is lower in
energy than would be expected in vivo, and the simulation brings the
structure back to a more normal state?
Thanks for any input,
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