Difference between revisions of "Loading OPTIM's min.data.info files into PATHSAMPLE"
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Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files. |
Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files. |
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| − | To do something useful lets compute the heat capacity as a function of temperature. |
+ | To do something useful lets compute the heat capacity as a function of temperature, based on the harmonic superposition approximation. |
1. Create two files min.A and min.B: |
1. Create two files min.A and min.B: |
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to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM). |
to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM). |
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| − | 3. Running PATHSAMPLE now should generate '''Cv.out''' with two columns - first |
+ | 3. Running PATHSAMPLE now should generate '''Cv.out''' with two columns - first for temperature and second for heat capacity. |
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| + | --[[User:Ss2029|Ss2029]] 14:46, 25 May 2011 (UTC) |
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Latest revision as of 14:28, 26 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, the final required files.
To do something useful lets compute the heat capacity as a function of temperature, based on the harmonic superposition approximation.
1. Create two files min.A and min.B:
> more min.A 1 1 > more min.B 1 2
2. In pathdata, comment out READMIN and add the CV command as
... comment READMIN min.data.info.initial CV 0.1 1.0 0.01 ...
to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM).
3. Running PATHSAMPLE now should generate Cv.out with two columns - first for temperature and second for heat capacity.
--Ss2029 14:46, 25 May 2011 (UTC)