I suggest using the nmropt option. See, for example, section 6.11.1 of the
AMBER11 manual.
Essentially you can do simulated annealing but in reverse. You can control
the heating with the annealing schedule.
--Dan
On Sat, Sep 11, 2010 at 5:59 PM, xqkong <xqkong.mail.shcnc.ac.cn> wrote:
> Dear amber users,
> I have a questions about how to control the speed of heating.I have a
> large system about 900 amino acids.In order to avoid large oscillations in
> energy and trajectory,i want to control the speed of heating (from 0k to
> 300K),but i don't know whether i should adjust the gamma_ln or use other
> method to control.Any suggestion will be much appreciated!
> Thanks in advance!
>
> Best regards,
>
> Xiangqian Kong
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Sat Sep 11 2010 - 02:30:05 PDT
