[gmx-users] Not enough ref_t and tau_t values!

[Aline Rossi]

Hi list,

Im dealing with a problem when trying to monitoring energygrps. When I
run the grompp i receive this output:
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 279 of the 1225 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 Protein_C 1
Excluding 2 bonded neighbours for SOL 30314
Excluding 1 bonded neighbours for NA+ 2
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 312 K
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   6825
#  G96ANGLES:   9964
#      PDIHS:   3583
#      IDIHS:   3430
#       LJ14:   10944
#     SETTLE:   30314
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 90944 elements
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: readir.c, line: 1131

Fatal error:
Not enough ref_t and tau_t values!

my index file is:
0 System              : 96772 atoms
  1 Protein             :  6694 atoms
  2 Protein-H           :  5213 atoms
  3 C-alpha             :   666 atoms
  4 Backbone            :  1998 atoms
  5 MainChain           :  2667 atoms
  6 MainChain+Cb        :  3268 atoms
  7 MainChain+H         :  3306 atoms
  8 SideChain           :  3388 atoms
  9 SideChain-H         :  2546 atoms
 10 Prot-Masses         :  6694 atoms
 11 Non-Protein         : 90078 atoms
 12 Mg                  :     7 atoms
 13 SOL                 : 90069 atoms
 14 NA+                 :     2 atoms
 15 Other               : 90078 atoms
 16 alpha&beta          :  6648 atoms
 17 his159              :    12 atoms
 18 arg157              :    17 atoms
 19 ecdw                :    51 atoms
 20 glu1                :    12 atoms
 21 cys2                :     8 atoms
 22 asp3                :     9 atoms
 23 trp4                :    22 atoms
 24 tyr458              :    18 atoms
 25 ala585              :     6 atoms
 26 prot+pep            :  6703 atoms
 27 prot+pep+mg         :  6706 atoms
 28 alpha               :  4453 atoms
 29 beta                :  2202 atoms
 30 pep                 :    51 atoms
title               =  PEP MD
cpp                 =  /lib/cpp
constraints         =  none
integrator          =  md
dt                  =  0.0015	; ps !
nsteps              =  10000000	; total 500 ps.
nstcomm             =  3000
nstxout             =  3000
nstvout             =  5000
nstfout             =  3000
nstlog              =  1500
nstenergy           =  3000
nstlist             =  5
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing          =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
unconstrained-start      = yes

; Berendsen temperature coupling is off in two groups
Tcoupl              =  berendsen
tc-grps		    =  alpha     beta      pep
tau_t               =  0.1       0.1       0.1
ref_t               =  312       312       312
; Energy monitoring
energygrps          =  alpha    beta    pep

; Isotropic pressure coupling is  on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

; Generate velocites is on at 312 K.
gen_vel             =  yes
gen_temp            =  312.0
gen_seed            =  173529

What should be wrong with my imputs??



Thanks for help
and my .mdp file is: