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, couldn´t it?
Thanks in advance
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Received on Thu Jul 05 2012 - 10:00:02 PDT
