[gmx-users] Re: About grompp problem: Not enough ref_t and ref_p values

[Monique Brito]

Hi!

I've added a newline at the end of the indexfile,
then the warning have vanished.
And the problem with fatal error is the same.
What can I do?

#####################################################################
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter
combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for UNk 1
WARNING 1 [file "rt.top", line 39]:
  System has non-zero total charge: 3.556006e+00

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution
at 300 K
renumbering atomtypes...
converting bonded parameters...
#      BONDS:   30753
#     ANGLES:   60152
#      PDIHS:   26940
#      IDIHS:   26630
#       LJ14:   55158
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing
2179 elements.

Fatal error: Not enough ref_t and tau_t values!
#####################################################################

Here is our md.mdp file.



title                    = 1rt1
include                  =
define                   = -DPOSRE
integrator               = md
dt                       = 0.001   ; 1 fs time
step
nsteps                   = 1000000 ; 1000 ps
simulation ou 1 ns
nstxout                  = 500
nstvout                  = 500
nstlog                   = 500
nstenergy                = 50
nstxtcout                = 0
energygrps               = UNK r_94 r_95 r_96
r_97 r_98 r_99 r_100 r_101 r_102 r_103 r_104
r_105 r_106 r_107 r_108 r_178 r_179 r_180 r_181
r_182 r_183 r_186 r_187 r_188 r_189 r_190 r_191
r_192 r_198 r_223 r_224 r_225 r_226 r_227 r_228
r_229 r_230 r_232 r_233 r_234 r_235 r_236 r_237
r_238 r_239 r_240 r_317 r_318 r_319 r_665 r_666
r_667 r_668
nstlist                  = 10  ; default value
ns_type                  = grid
rlist                    = 0.8
pbc                      = xyz
coulombtype              = PME
pme_order                = 4
optimize_fft             = yes
rcoulomb                 = 1.0
rvdw                     = 0.8
xtc_grps                 = UNK Protein_A
Protein_B
tcoupl                   = Berendsen
tc-grps                  = UNK Protein_A
Protein_B
tau_t                    = 0.1 0.1       0.1
ref_t                    = 300 300       300
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = none

The index group has the default elements plus
Protein_A and Protein_B atoms.

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