AMBER Archive (2007)

Subject: RE: AMBER: nscm in simulation annealing

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Fri Apr 13 2007 - 13:36:59 CDT

Dear Dr. Case,

There is "RE_POSITION Moving by" messages every nscm step in my output.

I do not understand why nscm can not be used when ntt=3 while ntt=1
should be used. If velocilies are not effected, it seems will not cause
any problem.

Thanks a lot,
Shaowen

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Friday, April 13, 2007 12:23 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: nscm in simulation annealing

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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