Hi jason,
Your guess is right. I run a parallel job using mpirun and pmemd rather than
pmemd.MPI.I will try it again using pmemd.MPI and see if the problem solved.
Thanks, Ibrahim
On Mon, Nov 3, 2014 10:56 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
On Mon, 2014-11-03 at 10:52 -0500, IBRAHIM M ABDELRADY wrote:
>> Hi,
>>
>>
>> I am trying to do an MD simulation of
>> a protein model using AMBER 12 using the following input for the
>equilibration
>> step:
>
>> The job is running using pmemd on a local cluster using 64 cpu. The run
>seemed to be OK; however,
>>
>>
>> looking at the output file I see a strange behavior. Some NSTEPs are
>written more than once and some are missing from the output file.
>>
>>
>> I extracted the "NSTEP" from the output (see below)
>and you can see that after NSTEP = 10500 ps, the program skipped NSTEP = 11000
>ps
>>
>>
>> and recorded NSTEP = 11500 followed by another NSTEP = 10500 ps. The same
>behavior is shown for other recorded NSTEP.
>>
>>
>> The same behavior happened in the heating step but the final coordinate
>file seemed to be OK and the time was recorded correctly at the header.
>>
>>
>> Not sure what might be wrong with the run? Any idea what is going on?
>>
>
>My guess is you are trying to run pmemd in parallel, but you are using
>"pmemd" instead of "pmemd.MPI". Of course since you didn't
>tell us how
>you actually tried to run the command, this is only a guess (but one
>that is consistent with what you've seen).
>
>Another possibility is that you are using a different MPI to run the
>simulation than the one used to compile Amber.
>
>HTH,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814)863 8703
Fax (814)865 7927
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 03 2014 - 08:30:03 PST
