Hi Bill,
I forgot to mention that I just get the Heat_01.out file. I'm not getting my .rst or .mdcrd files. In my Heat_01.out file there's no error, but it ends when finishing reading the input file (Heat_01.in). My guess is that there's something wrong in my Heat_01.in file. Because it looks like MD doesn't even start when the error happens.
Also, I don't think my restraints should be any problem. I have ran the same system with the same conditions in NAMD using AMBER forcefield and I haven't had any problems.
Daniela.
> On 4 Jul 2017, at 8:49 pm, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> 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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>
>
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Received on Tue Jul 04 2017 - 05:00:02 PDT
