Loading OPTIM's min.data.info files into PATHSAMPLE: Difference between revisions
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import>Ss2029 No edit summary |
import>Ss2029 No edit summary |
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cat min.data.info.* > min.data.info.initial |
cat min.data.info.* > min.data.info.initial |
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</pre> |
</pre> |
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In a new directory copy the following files: |
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<pre> |
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coords.inpcrd, coords.prmtop, min.data.info.initial, perm.allow, pathdata |
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</pre> |
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Listing of pathdata |
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<pre> |
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DEBUG |
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COPYFILES perm.allow min.in coords.inpcrd coords.prmtop |
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CLOSEFILES |
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NATOMS 22 |
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PERMDIST |
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SYSTEM AMBER |
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NAB |
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CONNECTIONS 1 |
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SEED 1 |
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PERTURB 0.40 |
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ETOL 1.0D-7 |
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GEOMDIFFTOL 0.1 |
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ITOL 1.0D0 |
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DIRECTION AB |
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EXEC /home/wales/bin/A9OPTIM |
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TRIPLES |
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ADDTRIPLES |
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STARTTRIPLES |
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CYCLES 0 |
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CPUS 1 |
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TEMPERATURE 0.59 |
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READMIN min.data.info.initial |
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</pre> |
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Running PATHSAMPLE now should generate '''points.min''' and '''min.data'''. |
Revision as of 14:33, 25 May 2011
Input files:
coord.1 to coord.N - N minima generated by GMIN + coords.inpcrd, coords.prmtop, perm.allow, min.in + odata, the optim input file
Listing of odata used with Amber OPTIM (exec A9OPTIM)
DEBUG UPDATES 6000 DUMPDATA ENDHESS MAXERISE 1.0D-4 1.0D0 BFGSMIN 1.0D-6 BFGSSTEPS 1000 MAXBFGS 0.2 NAB start POINTS
Run OPTIM on each GMIN minima and concatenate the resulting min.data.info files. Following script does this
# replace N with number of minima for i in $(seq 1 N) do echo $i cp coords.$i start /home/wales/bin/A9OPTIM mv min.data.info min.data.info.$i done # concatenate all min.data.info files cat min.data.info.* > min.data.info.initial
In a new directory copy the following files:
coords.inpcrd, coords.prmtop, min.data.info.initial, perm.allow, pathdata
Listing of pathdata
DEBUG COPYFILES perm.allow min.in coords.inpcrd coords.prmtop CLOSEFILES NATOMS 22 PERMDIST SYSTEM AMBER NAB CONNECTIONS 1 SEED 1 PERTURB 0.40 ETOL 1.0D-7 GEOMDIFFTOL 0.1 ITOL 1.0D0 DIRECTION AB EXEC /home/wales/bin/A9OPTIM TRIPLES ADDTRIPLES STARTTRIPLES CYCLES 0 CPUS 1 TEMPERATURE 0.59 READMIN min.data.info.initial
Running PATHSAMPLE now should generate points.min and min.data.