[gmx-users] Freezing problem

[Debashis Sahu]

Dear all,
           I can not freeze a group in mdrun in gas phase. Actually the
following error is coming in the grompp step................

Program grompp, VERSION 4.6.3
Source code file: /compile/gromacs-4.6.3/src/kernel/readir.c, line: 3192

Fatal error:
Invalid Freezing input: 1 groups and 1 freeze values
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I have tried also by taking the index file in grompp step, but same error
coming. My index file and mdp file are listed below. I want to freeze ABC
group while DDD will be free. In the topology I have inserted the molecule
DDD as DDD.itp..........If any mistake in the files there, plz help me.

*index.ndx file:*

[ System ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
 106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
 121  122  123  124  125  126  127  128  129
[ Other ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
 106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
 121  122  123  124  125  126  127  128  129
[ ABC ]
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98   99  100  101  102  103  104  105
 106  107  108  109  110  111  112  113  114  115  116  117  118  119  120
 121  122  123  124  125  126
[ DDD ]
 127  128  129

*mdp file:*

title = NVT equilibration
define = -DPOSRES ; position restrain the solute
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
freezegrps = ABC
freezedim =YYY
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = ABC  DDD ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300    ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
-- 
*Debashis Sahu*
*Central Salt and Marine Chemical Research Institute*
*Bhavnagar, Gujarat*
*India, 364002.*