[gmx-users] heat exchanges

[David van der Spoel]

XAvier Periole wrote:
> 
> On Feb 5, 2009, at 11:02 AM, Carlo Camilloni wrote:
> 
>> Dear Gromacs users,
>>
>> I am doing some tests with thermostats and I would like to know if 
>> someone has just done it. In particular:
> I have not done systematic tests but here are my impressions
>>
>> 1) How big has to be a protein to be coupled with a separate bath?
> a few residues ...
>>
>> 2) Do you know over which time scales a flux of heat is observed 
>> between protein and solvent using only one temperature group?
> few 10-100 ps.
This depends a lot on how the rest of the setup is, I would think. I had 
  some correspondence on the computational chemistry list about this 10 
years ago, and there people boldly stated that with Nose Hoover there is 
no need for coupling separate groups at all. At the time I could not 
reproduce that with GROMACS, but I did not persevere it. It could also 
have to do with flexibility, and/or using united atoms without charges, 
i.e. that there is little energetic coupling between e.g. water and a 
hydrophobic substance.

It would be worthwhile to do systematic tests with different thermostats 
and coupling schemes. If it turns out that the same problems exist in 
Nose Hoover thermostats then it is probably publishable as well.



>>
>>
>> Thanks,
>>
>> Carlo Camilloni
>>
>> -- 
>> Dr Carlo Camilloni
>> Department of Physics, University of Milano
>> via Celoria, 16 - 20133 Milano, Italy
>> phone: +39-02-50317654
>> carlo.camilloni at mi.infn.it
>> http://merlino.mi.infn.it/~carlo
>>
>>
>>
>>
>>
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se