Loading OPTIM's min.data.info files into PATHSAMPLE

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)