I have an explicitly solvated protein system for which I am attempting
to look at tens of nanosecond molecular dynamics using Sander.
Although the system appears to equilibrate well at first, I have been
unable to maintain constant temperature (at 300 K) upon switching from
ntt=3 to ntt=0. In previous simulations, the temperature increased
gradually from 298 K (after an initial dip) to 310 K over 30
nanoseconds. When I examined the energy profiles, I found that both
kinetic and potential energy are increasing throughout the ntt=0
simulations. I understand this to be an indicator of poor
equilibration, but I am unclear as to the cause of this sort of
problem in terms of the way the force field works.
Sally
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Received on Thu Oct 23 2008 - 23:45:10 PDT
