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
>> >>
>> >> _______________________________________________
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>> >>
>> >
>> >
>> >
>> >--
>> >Dr. Daniel J. Sindhikara
>> >Institute for Molecular Science
>> >E-mail: sindhikara.gmail.com
>> >Website: http://sites.google.com/site/dansindhikara/
>> >--
>> >_______________________________________________
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>> >
>> >
>>
>>
>>
>> Best regards,
>> Xiangqian Kong
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>>
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>
Best regards,
Xiangqian Kong
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Received on Sat Sep 11 2010 - 04:30:03 PDT
