Were there any error messages anywhere?
On Thu, Jul 5, 2012 at 12:50 PM, bmartini <bmartini.ibt.unam.mx> wrote:
> Hello Amber users,
> I have had some problems running entropy calculations using nmode with
> the following parameters.
> &general
> endframe=50, keep_files=2,
> /
> &nmode
> nmstartframe=5, nmendframe=45,
> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> /
> Something that strikes my attention is that the same script did not
> give any problem when the size of my complex was 2600 atoms but for the
> case of 6010 atoms, the calculation is not accomplished and when I
> review the progress.log file, the next information appears:
> Running MMPBSA.MPI on 4 processors
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> cpptraj found! Using
> /global/home/egarciah_g/egarciah/amber12/bin/cpptraj
> ptraj found! Using /global/home/egarciah_g/egarciah/amber12/bin/ptraj
> mmpbsa_py_nabnmode found! Using
> /global/home/egarciah_g/egarciah/amber12/bin/mmpbsa_py_nabnmode
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
> 9 frames were processed by cpptraj for nmode calculations.
> Beginning nmode calculations with
> /global/home/egarciah_g/egarciah/amber12/bin/mmpbsa_py_nabnmode
> calculating complex contribution...
>
> It looks like the process had been stopped and err file did not give
> any information. Someone who knows how to deal with this problem? It
> could be a system size problem, couldnīt it?
>
> Thanks in advance
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 05 2012 - 10:30:02 PDT
