Hi Yao Yao,
> I am treating a Heat Shock Protein with QMMMMD method. For different
> parts of the protein,
> I wonder if there is a way I can set different temperatures (or
> different temperature coupling methods) in my input file.
> And the temperature coupling plan does not necessarily overlap with the
> atom-separation plan for QMMM treatment.
No there is no way to do this in the input file. Such things, dual
thermostats etc, were removed a long time ago because they do not actually
represent anything physical and they were there mostly as a hack to deal
with poor energy conservation and coupling to the various degrees of freedom
etc.
That said it would probably not be too hard to modify the Berendsen
thermostat code to base the coupling constant on an atom based array so you
could have different coupling constants for the different atoms. The tricky
part is working out how to do mathematically this in a way that is
thermodynamically correct.
If you want to modify the code look for things like Temp0 and tautp - these
are read by mdread() from the cntrl namelist and then used throughout the
simulation. You could easily replace these (and the locations they are used)
with arrays based on atom number for example.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Wed Sep 21 2011 - 13:00:03 PDT
