yes it means the thermostat temperature changes continuously. of course your
real system will still have fluctuations.
On Sat, Sep 11, 2010 at 6:39 AM, xqkong <xqkong.mail.shcnc.ac.cn> wrote:
> Dear Daniel,
> Thanks for your suggestion! But i still have some puzzle.If i set the
> variables as below:
> &wt TYPE='TEMP0', istep1=0, istep2=50000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
> Does it mean that temperature is 0.1K at step1 and then it will change
> averagely and continuously for 50000 times to get the final temp of 300K?
> Thanks in advance!
>
> Daniel Sindhikara <sindhikara.gmail.com> at Sat, 11 Sep 2010 18:12:21
> wrote:
> >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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> 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/
> >--
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> Best regards,
> Xiangqian Kong
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Sep 11 2010 - 04:00:04 PDT
