[gmx-users] Number of degrees of freedom in T-Coupling group Protein is 0.00

Fernando Mattio mattiofer at gmail.com
Wed Feb 15 15:59:54 CET 2006

   Dear Gromacs users,
   Perhaps it is a simple question, but it will help me a lot. Is it
possible with GROMACS forcefield to simulate in a box elements without
solvent?? Or is the solvent an essential bondary condition?
   Well I could define a box with editconf and run simulations without using
genbox, in a system in which I froze some molecules and would like to have
the protein not frozen. However when running grompp I got the message
"Number of degrees of freedom in T-Coupling group Protein is 0.00" and
"Number of degrees of freedom in T-Coupling group OHH is 0.00" , and
probably as result of it the temperature was always zero.
   Below comes part of my .mdp file. I can not see why it occurs
(temperature = zero), once I believe that I applied the frozen group option
only for sol, not for protein. Can anybody help me? Sorry for the long
e-mail and thank you in advance for your colaboration,
   Fernando Mattio

;group(s) to write to xtc trajectory
xtc_grps         = protein  OHH
;group(s) to write to energy file
energygrps         = protein OHHl
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist          = 10
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type          = grid
;cut-off distance for the short-range neighbor list
rlist             = 0.8
;treatment of electrostatic interactions
coulombtype         = cut-off
rcoulomb         = 1.4
;treatment of van der waals interactions
rvdw             = 1.4
; Periodic boudary conditions in all the directions
pbc                      = xyz
;Temperature coupling
tcoupl           = berendsen
tc-grps          = protein OHH
tau_t             = 0.1 0.1
ref_t             = 263 263
;Pressure coupling
Pcoupl           = berendsen
Pcoupltype               = isotropic
tau_p             = 0.5
compressibility      = 4.5e-5
ref_p             = 1.0
;Velocity generation
gen_vel          = yes
gen_temp         = 263
gen_seed         = 173529
;Constrain all bonds
constraints         = all-bonds

freezegrps              = OHH
freezedim               = Y Y Y
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