Hi,
Try running in serial first with a smaller number of minimization
steps (~10-100) and print every step (ntpr=1). This will help ID
whether the problem is related to MPI or not.
-Dan
On Wed, Aug 14, 2013 at 9:59 AM, Moacyr Comar <mcomjr.gmail.com> wrote:
> Dr. David, thank you for the answer.
>
> The command line used is:
>
> $MPI_HOME/mpirun -np 4 $AMBERHOME/exe/sander.MPI -O -i min.in -o min.out -o
> box.top -c box.crd -r min.rst -ref box.crd
>
> The min.in is the same used in the tutorial:
>
> &cntrl
> imin=1, ntpr=100, ntwx=100, maxcyc=10000,
> ntb=1,
> &end
>
> Thanks again. Moacyr.
>
>
> 2013/8/12 David A Case <case.biomaps.rutgers.edu>
>
>> On Mon, Aug 12, 2013, Moacyr Comar wrote:
>> >
>> > I had tried run the simulations described in the tutorial A.15 (A room
>> > temperature ionic liquid) with amber9 and change the ionic liquid used in
>> > this tutorial by omin pf6. However, the minimization step do not produce
>> > any min.out at all when I use those commands and it does when I change
>> > ntb=1 for ntb=0 and igb=6. Does anyone have any idea how I can use
>> boundary
>> > conditions with the ionic liquid?
>> >
>> > the min.in of the tiutorial is:
>> >
>> > &cntrl
>> > imin=1, ntpr=100, ntwx=100, maxcyc=10000,
>> > ntb=1,
>> > &end
>>
>> We need to see the exact command line you used. There is generally no
>> reason for Amber to not create an output file (even if you inputs are
>> wrong; and lack of any output file has nothing to do with the nature of
>> the system you are running). Have you tried the usual: set maxcyc to 10,
>> ntpr to 1 and run the job interactively?
>>
>> ...dac
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Prof. Dr. Moacyr Comar Junior
> Universidade Federal de São João del Rei
> Campus Centro-Oeste
> Divinópolis - MG
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
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Received on Wed Aug 14 2013 - 09:30:03 PDT
