AMBER Archive (2007)

Subject: Re: AMBER: nscm in simulation annealing

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 13 2007 - 12:22:32 CDT

On Fri, Apr 13, 2007, Hu, Shaowen (JSC-SK)[USRA] wrote:

>
> And my temperature file is attached. If I set nscm=0, the
> temperature looks fine. I think it does effect the velocities.

Please if you have "RE_POSITION Moving by" messages in your output. It is not
clear yet whether or not there is indeed a bug here, or what is might be.
As I read the code, velocities should not be changed at nscm intervals.

Debugging this will require running *short* simulations, printing out
results at every step, and trying different values of nscm. Simulated
annealing is one area where ntt=1 is sometimes preferred, but ntt=3 should
work as well.

...dac

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