[gmx-users] about T-Coupling groups

[Rui Li]

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?




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