[gmx-users] Position Restrain Problem

[Anthony Cruz]

Hi users:
I am trying to run a simulation of the interaction between a protein that have 
two units and a small peptide. First I have the pdb file of the protein (2 
subunits) and the peptide. I use the -merge option of pdb2gmx to merge the 
two protein subunits in one topology and the peptide in other topology but 
all in the same .gro. I run the energy minimization without problem but it 
end too rapidly:

 Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    5.04580e+02    1.64344e+03    1.89068e+03    2.77582e+02    2.00071e+03
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    4.12043e+04    7.06859e+05   -1.90071e+04   -4.29975e+06   -4.75686e+05
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -4.04006e+06    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00

           Step           Time         Lambda
             27       27.00000        0.00000

           Step           Time         Lambda
             28       28.00000        0.00000

           Step           Time         Lambda
             29       29.00000        0.00000


Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 30 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -4.0400605e+06
Maximum force     =  2.5371721e+03 on atom 195774
Norm of force     =  5.4543950e+05

When I try to run the position restrain dynamics the process end abruptly. 
With this output from the log file :

Initializing LINear Constraint Solver
  number of constraints is 3992
  average number of constraints coupled to one constraint is 2.9

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.040178   2221   2222   0.006943
        After LINCS         0.000491   1144   1146   0.000052

Going to use C-settle (4728 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837
rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.093162   2933   2934   0.016557
        After LINCS         0.000218   1271   1273   0.000034

Started mdrun on node 0 Mon Dec 19 09:31:45 2005
Initial temperature: 298.48 K
           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 20 x 20 x 20 cells
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.066290   2460   2461   0.005114
        After LINCS         0.000133   1144   1146   0.000015

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    2.01626e+03    1.90234e+03    3.07489e+02    2.05943e+03    4.13328e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR) Position Rest.
    7.08229e+05   -1.90024e+04   -4.30085e+06   -5.03389e+05    1.49338e+06
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -2.57402e+06    7.21568e+05   -1.85245e+06    2.99867e+02   -1.16469e+03


t = 0.020 ps: Water molecule starting at atom 3923 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.036 ps: Water molecule starting at atom 7658 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.038 ps: Water molecule starting at atom 7703 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.040 ps: Water molecule starting at atom 8420 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.042 ps: Water molecule starting at atom 7724 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates


And the following output from the pbs errors file: 

starting mdrun 'HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR'
300000 steps,    600.0 ps.

step 0
Wrote pdb files with previous and current coordinates
step 10, will finish at Wed May 31 14:12:32 2006
Wrote pdb files with previous and current coordinates

Back Off! I just backed up step17.pdb to ./#step17.pdb.1#
Wrote pdb files with previous and current coordinates

Back Off! I just backed up step18.pdb to ./#step18.pdb.1#
Sorry couldn't backup step18.pdb to ./#step18.pdb.1#

Back Off! I just backed up step19.pdb to ./#step19.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Back Off! I just backed up step19.pdb to ./#step19.pdb.2#
Wrote pdb files with previous and current coordinates
step 20, will finish at Sat Apr  7 06:34:59 2007

Back Off! I just backed up step20.pdb to ./#step20.pdb.1#
Sorry couldn't backup step20.pdb to ./#step20.pdb.1#

Back Off! I just backed up step21.pdb to ./#step21.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
MPI: On host caffenero.hpcf.upr.edu, 
Program /usr/local/gromacs/ia64-unknown-linux-gnu/bin/mdrun_mpi, Rank 15, 
Process 31770 received signal SIGSEGV(11)


MPI: --------stack traceback-------
sh: line 1: idb: command not found

MPI: -----stack traceback ends-----
MPI: On host caffenero.hpcf.upr.edu, 
Program /usr/local/gromacs/ia64-unknown-linux-gnu/bin/mdrun_mpi, Rank 15, 
Process 31770: Dumping core on signal SIGSEG
V(11) into directory /home/acruz/asv.31738
MPI: MPI_COMM_WORLD rank 15 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 11

What could be the problem???