From NWChem
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Just Got Here
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| 12:45:12 PM PST - Fri, Dec 27th 2013 |
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I am having a hard time creating an input file for an Optimization task. Here is the input I have so far. I have never worked with nwchem before.
title "Prepare QM/MM calculation of 3SPI.pdb"
start 3SPI
prepare
- --name of the pdb file
source 3SPI.pdb
- --generate new topology and sequence file
new_top new_seq
- --generate new restart file
new_rst
- --define quantum region (note the use of underscore)
modify segment 400 quantum
modify segment 78 quantum
modify segment 80 quantum
modify segment 186 quantum
- fix residues more than 20 A away from Potassium atom
fix segments beyond 2.0 1:_C1A
update lists
ignore
end
task prepare
md
- this specifies that 3SPI_md.rst will be used as a restart file
- and 3SPI.top will be a topology file
system 3SPI_md
end
qmmm
[ eref <double precision default 0.0d0>]
[ bqzone <double precision default 9.0d0>]
[ mm_charges [exclude <(none||all||linkbond||linkbond_H) default none>]
[ expand <none||all||solute||solvent> default none]
[ update <integer default 0>]
[ link_atoms <(hydrogen||halogen) default hydrogen>]
[ link_ecp <(auto||user) default auto>]
[ region < [region1] [region2] [region3] > ]
[ method [method1] [method2] [method3] ]
[ maxiter [maxiter1] [maxiter2] [maxiter3] ]
[ ncycles < [number] default 1 > ]
[ density [espfit] [static] [dynamical] default dynamical ]
end
task qmmm optimization
this is part of the long error message I got:
mpirun has exited due to process rank 0 with PID 1618 on
node r1i1n5 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
libc.so.6 00002AE0FCDE96A7 Unknown Unknown Unknown
libmpi.so.1 00002AE0FBDC0425 Unknown
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