Hi,
I am using the MMPBSA.py.MPI script included in amber 11 on a computing
cluster. Unfortunately, it sometimes happens that jobs are stopped or
get rescheduled for administrative reasons beyond my control.
In the MMPBSA.py documentation, I cannot find any info on how to restart
them in an intelligent way without beginning from scratch.
For example, one job is started with the input file:
Input File for running PB and GB
&general
startframe=4750,
endframe=5000,
interval=1,
keep_files=0,
/
&gb
igb=5,
saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=3,
print_res="33-38; 41; 149; 152-153; 176-183; 204"
dec_verbose=3,
/
It is run on several nodes in parallel with MMPBSA.py.MPI. There is only
one restrt file present in the directory; and the temp files startin
with _MMPBSA_.
* Can I use the restrt (or some other temp file) to continue from where
the job stopped?
* when the GB calculations are already done, can I create an output file
(like FINAL_RESULTS_MMPBSA.dat) from the _MMPBSA_receptor_gb.mdout.X
_MMPBSA_ligand_gb.mdout.X _MMPBSA_complex_gb.mdout.X files?
Thanks,
Chris
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Received on Fri Apr 01 2011 - 07:30:02 PDT
