[gmx-users] how warm and later relax one system?
k.a.feenstra at chem.rug.nl
Fri Dec 14 10:52:05 CET 2001
David van der Spoel wrote:
> On Thu, 13 Dec 2001, Geraudis Mustelier wrote:
> >I am a new user of gromacs, and being frank, I have relatively little
> >experience in the energy's calculations (energy minimization of and
> >molecular dynamics). So far, I have a small doubt that I would like that
> >somebody explain me.
> >I want to evaluate different conformations from a particular region of a
> >protein molecule, the rest of the molecule is fixed. In general, to warm the
> >system, is to say, set initial temperature relatively high. Later, allow to
> >the system relax until arrive at a room temperature, perhaps 300K or smaller
> >one. Therefore, the system would journey across different local states of
> >minimum energy or perhaps it would arrive to the absolute minimum.
> >That is possible? Which parameters must be appear in the file (.mdp) to
> >obtain this simulation?
> Yes using simulated annealing. It is described in the manual. You give a
> starting temperature, say 600 K, and then a time at which the temperature
> should be zero.
Which can also be negative, causing the system to heat.
| | Anton Feenstra Dept. of Biophysical Chemistry |
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