[gmx-users] about T-Coupling groups

[David van der Spoel]

Rui Li wrote:
> Dear all,
> I want run a Position-restrained dynamics simulation for my system
> and I write a pr.mdp file.
> 
> below is part of the mdp file:
> 
> Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.1       0.1     0.1
> tc-grps             =  Protein   SOL     Cl
> ref_t               =  300       300     300
> ; Energy monitoring
> energygrps          =  Protein  SOL  Cl
> ; Pressure coupling is not on
> Pcoupl              =  berendsen
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>                                                                                   
>                                           
> 
> 
> When I use grompp, it warns:
> 
> Fatal error:
> 149 atoms are not part of any of the T-Coupling groups
> 
> what's wrong with it?
> 
check the archives.

David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++