[gmx-users] ligand temperature in MD

[K.A.Feenstra]

Ivano Eberini wrote:
> 
> Hi,
> 
> we have just finished running 3 ns MD for a lipocalin (fatty acid
> binding protein) with one of its ligands (oleate). Berendsen temperature
> coupling was switched on in three groups: protein, SOL and DRG (oleate)
> with tau_t = 0.1 and ref_t = 300. If we take a look at temperature
> during MD, we obtain an RMSD of 1-2 % for protein (T-Protein) and water
> (T-SOL), but things are quite different for the ligand, oleate, (T-DRG).
> What can be the reason for this result?

Quite simple, temperature coupling is not exact, i.e. instantaneous
temperatures will deviate from the thermostat setting. This is more
obvious for smaller groups of atoms, also due to the relatively large
interactions a small group of atoms has with its surroundings. Also,
for charged molecules (like, possibly, your ligand), there can be
additional energetic effects that cause a response in temperature.

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
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