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

Geraudis Mustelier gera at ict.cim.sld.cu
Thu Dec 13 19:25:53 CET 2001


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?


 MSc. Geraudis Mustelier-Portuondo

 Center of Molecular Immunology
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 email: gera at ict.cim.sld.cu

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