[gmx-users] ligand temperature in MD

[Ivano Eberini]

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?

Thanks in advance.

Best regards,

Ivano Eberini

***

Statistics over 1500001 steps [ 0.0000 thru 3000.0002 ps ], 1 data sets

Energy                      Average       RMSD     Fluct.      Drift  
Tot-Drift
-------------------------------------------------------------------------------
T-Protein                   300.139    6.54478    6.54461 5.56907e-05   
0.167072
T-SOL                       314.788    2.01884    2.01862 3.42209e-05   
0.102663
T-DRG                       293.456    45.2639    45.2582 -0.000833777   
-2.50133

--
Ivano Eberini
Laboratorio di Farmacologia del Diabete
Dipartimento di Scienze Farmacologiche
Università degli Studi di Milano
Via G. Balzaretti, 9
20133 - Milano
Tel.: +39025835-8304/-8359 Fax: +390258358284

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