[gmx-users] Estimated temperature by gmxchek

[Anton Feenstra]

Ester Chiessi wrote:
> Hi,
> 
> I'd like to perform MD of a polymeric network in SCP water, mantaining
> chemical bonds across boundaries in PBC.
[...]
> I found very strange the temperature! The number of degrees of freedom of my
> system should be Natoms * 3 ( I only correct for the center of mass motion),
> or not?

Constraints (e.g. Settles and Shake/Lincs) remove degrees of freedom.
You'll need to count them and subtract them from Natoms*3 - 6 (rotation
and motion of the whole system are not possible).

> The 309.708 K value seems too far from 303 K, too.



-- 
Groetjes,

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