Dear Carlos£¬
Thanks for your suggestion!But i still have some puzzle,you mean that
all the TEMP controls is the bath temperature.If the temperature
heat from 200K to 300K ,does the temp of bath also heat from 200k to
300k?or the temp of bath is always 300K?
Meanwhile ,Does nmropt is used for ntt=1 rather than ntt=3? If i want to
control the speed of heating,do i vary the value of TEMP0 or TAUTP
as nmropt=1?
Thanks in advance!
Carlos Simmerling <carlos.simmerling.gmail.com> at Sat, 11 Sep 2010 07:01:51 wrote:
>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
>>
>_______________________________________________
>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
Received on Sat Sep 11 2010 - 23:30:03 PDT
