the fluctuations depend on which thermostat you use. all the TEMP controls
is the bath temperature.
my personal preference is never to heat from such a low temperature. I find
it perfectly acceptable to assign an initial T of about 200K (still very
cold) and heat from there.
On Sat, Sep 11, 2010 at 6:59 AM, xqkong <xqkong.mail.shcnc.ac.cn> wrote:
> Dear Carlos,
> Thanks for your suggestion! In your opinion , what can i do to prevent
> large fluctuations ? I think maybe i can set the istep2 larger to slow the
> speed of heating to avoid this partly.
> Thanks in advance!
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com> at Sat, 11 Sep 2010
> 06:40:30 wrote:
> >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
> >>
> >_______________________________________________
> >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 - 04:30:04 PDT
