[gmx-users] molecular dynamics problems

[Anton Feenstra]

Xavier Periole wrote:
>> When I measured the temp. of the solute molecule (only 41 atoms from 4850
>> of the whole system)it was even lower then solvent temp., which led me to
>> belive that I have a 'hot solvent, cold solute situation' From your
>> experience what is the normal variation of local temp.(compared to total
>> temp.) in a well behaved simulation?
>>
> A solvent at 200 K and a solute at <200K and the full system 300K !!!! 
> Something is definitely wrong.

The number of degrees of freedom (nrdf) come into calculating the temperature.
E.g., for one constraint per atom (i.e., bond-length), you remove one of its
three degrees of freedom. Taking that into accoount, that will change the
temperature by 3/2, and would raise 200K to 300K.

I would not be surprised if in the calculation of the system temp, nrdf
*is* taken into account, but not for the 'local' temp. It may be a
feature (if it does what it sais in the manual, I don't know that), or
else it is a bug.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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