Hi all,
I'm a new amber user and I'm having problems running heating after
minimization. I didn't have any issues when running the minimization with
MPI, but I'm having problems when trying to continue with heating.
My input file is:
Membrane-Protein Heating Step 1
&cntrl
imin = 0, ! No Minimization
ntx = 1, ! Positions read with no initial velocities
irest = 0, ! No Restart
scee = 1.2, ! Scaling factor for 1-4 elesctrostatic interactions
cut = 12, ! Cut-off for vdW and electrostatic interactions
ntc = 2, ! SHAKE on for bond with hydrogen
tol = 0.0005, ! SHAKE tolerance
ntf = 2, ! No force evaluation for bonds with hydrogen
ntt = 3, ! Langevin thermostat
gamma_ln = 5, ! Damping coefficient for Langevin dynamics
ig = -1, ! Random seed for Langevin thermostat
ntp = 0, ! No pressure scaling
ntb = 1, ! Constant volume
ntr = 1, ! Restrain atoms using a harmonic potential
nmropt = 1, ! NMR restraints will be read
nstlim = 5000, ! Number of MD steps
dt = 0.002, ! Timestep in ps
ntpr = 100, ! Print to mdout every ntpr steps
ntwx = 100, ! Write to trajectory file every ntwx steps
ntwr = 1000, ! Write a restart file every ntwr steps
ioutfm = 1, ! Write a binary trajectory
ntxo = 2, ! Write binary restart files
/
&wt
type = 'TEMP0', ! Varies the target temperature TEMP0
istep1 = 0, ! Initial step
istep2 = 5000, ! Final step
value1 = 0, ! Initial temp0 in K
value2 = 100 ! Final temp0 in K
/
&wt
type = 'END'
/
Hold lipid fixed
30 ! Force constant
RES 456 1592 ! Lipid residues
END
Protein Backbone C
30 ! Force constant
FIND
C * * *
SEARCH
RES 1 453
END
Protein Backbone N
30 ! Force constant
FIND
N * * *
SEARCH
RES 1 453
END
Protein Backbone CA
30 ! Force constant
FIND
CA * * *
SEARCH
RES 1 453
END
Protein Backbone O
30 ! Force constant
FIND
O * * *
SEARCH
RES 1 453
END
Glucose
30
RES 454 455
END
END
My PBS file is:
#!/bin/bash
#PBS -q normalbw
#PBS -P r16
#PBS -l ncpus=56
#PBS -l walltime=02:00:00
#PBS -l mem=8GB
#PBS -l software=amber
#PBS -l other=mpi
#PBS -l wd
module load openmpi/1.6.3
module load amber/16-16.05
mpirun -np $PBS_NCPUS $AMBERHOME/bin/pmemd.MPI -O -i Heat_01.in -o
Heat_01.out -p GLUT3_InOpen.prmtop -c Min.rst -r Heat_01.rst -ref Min.rst
-x Heat_01.mdcrd
And the error I get is:
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[56289,1],0]
Exit code: 19
I have been all day trying to figure out what is wrong but I can't find the
error. Any ideas?
Thanks in advance,
Daniela.
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Received on Tue Jul 04 2017 - 04:00:02 PDT
