[gmx-users] how warm and later relax one system?

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 13 21:03:07 CET 2001

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.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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