Hello,
I believe that the only part of the calculation that really uses the
temperature are the entropy calculations. You can see that the temperature
is defined in mm_pbsa_statistics.pm, and you can change it there (look for
TEMP). However, take care if you're looking to change the temperature for
entropy calculations, as the temperature 298.15 is hard-coded into the
source codes of both nmode and nab. Therefore, changing the temperature
requires you to change the default value in every location that uses the
temperature and then recompiling the corresponding programs that you
changed, then re-running the mm_pbsa simulations. There may be pieces here
that I'm missing, but I think I got the important ones.
Hope this helps,
Jason
2010/8/10 pxq <pangxueqintea.yahoo.com.cn>
> Hello everyone,
>
> I am using mm_pbsa.pl to calculate the binding free energy between
> the ligand and protein. But the given temperature of mm_pbsa.pl is 300K
> while my simulation temperature is 310K, is it ok to use 300K to calculate?
> If not, how to change temperature in the input script? Cause there is no
> such option so far as I know.
>
> Thanks ahead for your kind help
>
> Xueqin
>
>
>
>
> =============================================================================================================
> Pang Xueqin
> State Key Laboratory of Molecular Reaction Dynamics
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: 0411-84379352
> Mobile: 15840973721
> Fax: 0411-84675584
> E-mail: pxq.dicp.ac.cn
> http://english.dicp.cas.cn/
>
> =============================================================================================================
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Aug 11 2010 - 08:30:05 PDT
