[gmx-users] Position Restrain Problem
Andrea C. Vaiana
vaiana at lanl.gov
Mon Dec 19 22:01:09 CET 2005
I had a similar problem and it turned out that in my coordinate file
atoms were ordered differently than in the topology file...
check if grompp gives a warning when reading in the topology and
coordinates.
Andrea
On Dec 19, 2005, at 1:08 PM, Anthony Cruz wrote:
> 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???
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