spoel at xray.bmc.uu.se
Thu Feb 13 17:02:58 CET 2003
On Thu, 2003-02-13 at 17:46, Alan Wilter Sousa da Silva wrote:
> Hi List!
> In a MD, I would like to start a system from a very small
> temperature and so heating it in about 100 ps until 300k and then
> stabilising there for some ns. All that instructions in the *.mdp file.
> I read about simulated annealing in the manual but it said
> "Negative zero_temp_time results in heating, which will go on
> indefinitely." (p. 125).
> Otherwise, I start with zero velocities and Berendsen coup.
> temp. set to 300k. However it takes less than 1ps to achieve 300k.
> Could someone give another suggestion?
Do the simulation in two steps. Be sure not to generate velocities in
the second simulation, and to turn off initial shake.
> Many thanks in advance.
> Alan Wilter S. da Silva
> Laboratório de Física Biológica
> Instituto de Biofísica Carlos Chagas Filho
> Universidade do Brasil/UFRJ
> Rio de Janeiro, Brasil
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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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