Make sure that you use correct solvated topology. (Tips: Try googling IFBOX == 0)
Cheers
Hai
> On Sep 28, 2016, at 10:47 AM, Pooja Kesari <pkesari88.gmail.com> wrote:
>
> Dear David,
> My parameters are
> molecular dynamics production run
>
> &cntrl
>
> imin=0, ntx=5,irest=1,
>
> ntb=2,cut=10.0,
>
> ntp=1,
>
> ntc=2,
>
> ntf=2,
>
> ntt=3, temp0=300.0, gamma_ln=2.0,
>
> nstlim=5000000, dt=0.002,taup=2.0,
>
> iwrap=1,ioutfm=0,
>
> ntpr=1000, ntwr=50000, ntave=1000, ntwx=1000,
>
> ig=-1,
>
> /
>
> my prod_complex-solv.out file says
>
> | MPI Timing options:
> | profile_mpi = 0
>
> (NTB /= 0 && NTP /= 0) but IFBOX == 0
>
> This combination is not supported
>
> *** input error(s)
>
> Can you please suggest something??
>
> On Wed, Sep 28, 2016 at 6:39 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>>> On Wed, Sep 28, 2016, Pooja Kesari wrote:
>>>
>>> *I m trying to run a production run*
>>> mpirun -np 8 sander.MPI -O -i prod.in -o prod_complex-solv.out -p
>>> complex-pose8.prmtop -c protein_solv-equil.rst -r protein_solv-prod.rst
>> -x
>>> prod.mdcrd -ref protein_solv-equil.rst
>>>
>>> *However my program is terminating with an error*
>>>
>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>
>> You need to look in the output files for indications about the error
>> messages.
>> The above message just says that the job failed.
>>
>> With sander.MPI, try to see if the problem occurs right at the end (after
>> the
>> MD is finished, and while the program is trying to print the timings on
>> various nodes...we've seen some problems with some MPI's on that.
>>
>> If possible, run with pmemd.MPI instead of sander.MPI.
>>
>> ...dac
>>
>>
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>
>
>
> --
> Thanks & Regards,
> Pooja Kesari
> Research Scholar
> Department Of Biotechnology
> Indian Institute of Technology Roorkee
> INDIA
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Received on Wed Sep 28 2016 - 08:30:02 PDT
