I suggest trying to run 1000 steps at 10K without restraints, to see if
the problem is with your restraints or your model.
Also, see the end of your mdout for clues.
Bill
On 7/4/17 3:34 AM, Daniela Rivas wrote:
> 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 - 04:00:03 PDT
