You can check the status of the calculation by looking at the output files
generated (it's most likely on the normal mode part, so you can look at
_MMPBSA_complex_nm.out.# or the corresponding file for the receptor or
ligand).
You can also look at the last time a file has been modified. This should
tell you if the program crashed or not -- if there has been nothing written
there for a day or so, it has likely crashed. Otherwise, it may just be
taking a **very** long time to minimize close enough to a local minimum to
be happy.
HTH,
Jason
On Tue, Jun 12, 2012 at 12:02 AM, Cao Yang <muxiachuixue.163.com> wrote:
> Hi all,
> I am using Amber11 and AmberTools 1.5. 10 ns simulations of an inhibtor
> with protein A and B have been conducted respectively. There are about 350
> AA in each complex. The common input file of complex A and B is as
> following:
>
> Input file for running entropy calculations using NMode
> &general
> startframe=3500, endframe=5000, keep_files=2, interval=10,
> /
> &nmode
> nmstartframe=1,
> nminterval=10, nmode_igb=1, nmode_istrng=0.1,
> /
>
> Here is the comand line:
> mpirun -np 12 MMPBSA.MPI -O -i mmpbsa.in -o MMPBSA.dat -sp com_sol.prmtop
> -cp com_solv.prmtop -rp receptor.prmtop -lp ligand.prmtop -y ../com.mdcrd
>
> It takes about 3 days to finish the NMode entropy calculation of 15 frames
> of complex A's trajectory.
> The problem is, in complex B's case, the CPU numebers reduced from 12 to 8
> abnormally and it has been 7 days till now. While the job is still
> running. Should I wait or kill the task? Why did this phenomenon happen?
>
> Many thanks.
>
> Cao Yang,
> Zhejiang University.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 12 2012 - 04:30:04 PDT
