One can also use the protocol for controlling heating of the system
described in: M.Gallo, et al. Novel procedure for thermal equilibration in
molecular dynamics simulation, Molecular Simulation, 35(5), 349-357, 2009.
Essentially the heating is done by controlling the temperature of water bath
only. When the temperature of water and solute become the same then the
entire system is equilibrated. Unfortunately this protocol is realizable
only in NAMD so far.
Piotr Cieplak
> 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 - 23:00:03 PDT
