[gmx-users] Coupling groups - Thermostat

Steven Neumann s.neumann08 at gmail.com
Tue Jan 10 16:52:02 CET 2012

Dear Gmx Users,

My system includes: ions, water, two tubes made of carbon atoms, protein.
I would like to run NVT (and then NPT) with position restarined dynamics of
my protein and tubes.
I am wondering whether this approach is good (two coupling groups:
Protein_Tubes and Water_and_ions??

My thermostat in mdp file:

 Temperature coupling is on

tcoupl = V-rescale ;

tc_grps = Protein_Tubes Water_and_ions ; two coupling groups

tau_t = 0.1 0.1 ; time constant

ref_t = 298 298 ; reference temperature

Please, let me know whether this apporach is ok. How can I set tc_grps when
I want to add ligand?

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