Hi,
On Wed, Aug 14, 2013 at 12:08 PM, Moacyr Comar <mcomjr.gmail.com> wrote:
> I tried to run the Dan's suggestion and I got the message of segmentation
> fault when I used the min.in proposed in the tutorial but when I changed to
> ntb=0 and igb=6 the minimization works well. I send the box.top and the
> box.crd for any test.
Minimizing your periodic system with ntb=0 is probably not what you
want. The biggest issue with this is that when ntb=0 sander/pmemd have
no concept of periodic boundaries, so molecules can go flying off into
space. Then if you try to simulate with periodic boundaries on using
those coords you will likely get some strange clashes/behavior.
That being said I can reproduce the segfault. I'll look into it
further and let you know what I find.
-Dan
>
> Any suggestion is very welcome!!!
>
> Thanks for all!!
>
>
> 2013/8/14 Jason Swails <jason.swails.gmail.com>
>
>>
>>
>> On Aug 14, 2013, at 8:59 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
>>
>> What error message did you get? My guess is that mpirun is in
>> $MPI_HOME/bin, not $MPI_HOME. That is if you even have the $MPI_HOME
>> environment variable set.
>>
>> There are so many possible places that the error can come up that we
>> cannot hope to narrow it down to a single cause with the information we
>> have.
>>
>> Dan's suggestion to run in serial first is a good one, and is typically a
>> good first step when debugging a problem.
>>
>> HTH,
>> Jason
>>
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>>
>
>
>
> --
> Prof. Dr. Moacyr Comar Junior
> Universidade Federal de São João del Rei
> Campus Centro-Oeste
> Divinópolis - MG
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Wed Aug 14 2013 - 15:30:02 PDT
