Simplification is a strategy available to you, if you want to try it.
Bill
On 7/4/17 4:36 AM, Daniela Rivas wrote:
> 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.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Jul 04 2017 - 05:00:03 PDT
