# [gmx-users] molecular dynamics problems

Thu Jul 22 12:45:50 CEST 2004

```Dear Anton

Thanks for giving me a new perspective on my problem. Until now I was
clueless about what was happening and that disturbed me a lot. So if I get
it rigth T = 2*Ekin/k*(3N-Nc) and considering that I have SHAKEd 3200
hydrogens, from the total of 3*4800 degrees of freedom = 14400 it leaved
me with only 11200 dof, and 11200/14400=0,77 wich from 300k means 230K,
the rest being probably from not enough equilibrated system.

BTW in your opinion how much will deviate local temp. in a good simulation
from overall temp. ? 5-10K maybe ?

Looking in Sybyl's manual I see that they calculate so: T=
2k*Ekin/(3N-Nc-3),and nothing is told about local temp.BTW I hope that
Boltzman's k is misplaced only in the text books and not in the algorithm
:-).

I will pass this hint to Sybyl developers, until now they were a little
slughish in there response.

Many thanks and best regards

> 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 |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> |             | "If You See Me Getting High, Knock Me Down"           |
> |             | (Red Hot Chili Peppers)                               |
> |_____________|_______________________________________________________|
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```