Dear Amber users;
I am running amber 10 on a linux cluster (12 cores/node, intel Xeon EP X5660, with 24GB of RAM per node). When I run an LMOD calculation to mimic an induced fit calculation, I use the following restraint mask to restrain residues beyond 6 A of a ligand: restraintmask=':413 > .6.0 '. All goes well, but if I increase the radius to 10A instead of 6A, the error below occurs. Also, very large energies occur on the last report on the output file (shown below the error message). Any ideas of what might cause the error or any suggestions on how to resolve it? The corresponding input file text follows the error message.
srun: mvapich: 2012-12-17T15:57:28: ABORT from MPI rank 0 [on sierra494]
ERROR in load_lbfgs(): YS=0.
[0] [MPI Abort by user] Aborting Program!
[0:sierra494] Abort: MPI_Abort() code: 1, rank 0, MPI Abort by user Aborting program !: at line 97 in file mpid_init.c
slurmd[sierra494]: *** STEP 95300.0 KILLED AT 2012-12-17T15:57:28 WITH SIGNAL 9 ***
slurmd[sierra495]: *** STEP 95300.0 KILLED AT 2012-12-17T15:57:28 WITH SIGNAL 9 ***
slurmd[sierra496]: *** STEP 95300.0 KILLED AT 2012-12-17T15:57:28 WITH SIGNAL 9 ***
srun: error: sierra495: tasks 11-21: Killed
srun: error: sierra494: task 0: Exited with exit code 255
srun: error: sierra494: tasks 1-10: Killed
srun: error: sierra496: tasks 22-31: Killed
srun: Force Terminated job step 95300.0
The end of the output file:
....
....
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
75 -7.8417E+07 2.2520E+12 1.6224E+14 HG1 4185
BOND = 477.7534 ANGLE = 1713.7025 DIHED = 4111.8065
VDWAALS = -2986.7942 EEL = -29227.3389 EGB = -4925.0859
1-4 VDW = 1476.0553 1-4 EEL = ************* RESTRAINT = 342.4850
EAMBER = *************
End of LMOD requested XMIN relaxation
Start of LMOD requested XMIN minimization
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -7.8417E+07 2.2520E+12 1.6224E+14 HG1 4185
BOND = 477.7534 ANGLE = 1713.7025 DIHED = 4111.8065
VDWAALS = -2986.7942 EEL = -29227.3389 EGB = -4925.0859
1-4 VDW = 1476.0553 1-4 EEL = ************* RESTRAINT = 342.4850
EAMBER = *************
XMIN ERROR: Status is -4
Input file:
Title..
&cntrl
imin = 1,
ntx =1,
maxcyc = 2000,
ncyc = 2100,
ntb = 0,
ntmin=4,
ntpr=1,
ntr=1,
ntrx=1,
igb = 5,
cut = 15,
ntr=1,
restraint_wt=100,
restraintmask=':413 > .10.0 '
/
&lmod
conflib_size = 30,
number_lmod_iterations = 30,
total_low_modes = 10,
explored_low_modes = 5,
number_free_rotrans_modes = 0,
energy_window = 50.0,
lmod_minimize_grms = 0.1,
arnoldi_dimension = 50,
matrix_vector_product_method = 'forward',
frequency_eigenvector_recalc = 6,
lmod_restart_frequency = 5,
restart_pool_size = 3,
number_lmod_moves = 0,
lmod_step_size_max = 5.0,
lmod_step_size_min = 2.0,
lmod_relax_grms = 1.0,
Monte_Carlo_method = 'Metropolis',
rtemperature = 1.5,
number_ligands = 1,
ligstart_list = '[]',
ligend_list = '[]',
ligcent_list = '[0]',
rotmin_list = '[20]',
rotmax_list = '[180]',
trmin_list = '[0.1]',
trmax_list = '[1.0]',
frequency_ligand_rotrans = 1,
number_ligand_rotrans = 5,
conflib_filename = 'Fluxetine.1.lmod_dock_conflib',
lmod_trajectory_filename = 'Fluxetine.1.lmod_dock_trajectory',
lmod_job_title = 'Fluxetine.1 lmod-dock test job',
lmod_verbosity = 2,
random_seed = 314159,
lbfgs_memory_depth = 3,
xmin_method = 'LBFGS',
xmin_verbosity = 0
/
Thanks in advance;
-Sergio
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Received on Mon Dec 17 2012 - 16:30:03 PST
