AMBER Archive (2009)
Subject: Re: [AMBER] Simulated annealing
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Apr 24 2009 - 09:49:40 CDT
hard to say without knowing more details. is it a standard system, or
modified force field?
did it go up in a continuation run, or a new run? what were the energies like?
at high T you may well need smaller time steps (2fs or 0.5fs).
also be VERY careful at 1000K, you will almost certainly need
restraints on amides, chirality and so on. details depend on your
molecule, but don't expect any chiral centers or cis/trans double
bonds to stay the same at that temperature.
On Fri, Apr 24, 2009 at 10:31 AM, waleed zalloum
> Dear Amber users,
> I am running simulated annealing, In my input file I heat the system up to 1000K and then cool it slowly. It was running well, but today I used the same input file and the temperature keeps going up to many thousands of K (~ 10000K).
> Anyone faced such a problem?
> Thank you in advance
> AMBER mailing list
AMBER mailing list