Relaxing existing minima with new potential and creating new database

Sometimes it may happen that you need to change potential. All minima that you found using previous potential can be relaxed in new potential and you do not need to start your job from the very beginning!

There is a simple way to do it. First you need to extract coordinates of all minima from binary file points.min and minimize each structure using new potential, and then you have to create new points.min file.

Here is a step-by-step recipe:

0. update potential - in case of AMBER users it means new topology file

1. create subdirectory relax_min

 mkdir relax_min

2. copy some files to that subdirectory:

AMBER users:

 cp points.min min.data odata.start perm.allow coords.prmtop coords.inpcrd min.in relax_min

CHARMM users:

 cp points.min min.data odata.start perm.allow input.crd relax_min

3. change name of odata.start into odata

 mv odata.start odata

4. AMBER users: create script relax as follows:

 #!/bin/csh
 
 set count = 1
 
 while ($count < 621)
 
    echo NATOMS 3002 > pathdata
    echo COPYFILES coords.prmtop coords.inpcrd min.in >> pathdata
    echo AMBER9 >> pathdata
    echo EXTRACTMIN $count >> pathdata
    /home/wales/bin/pathsample.2.1 >& pathsample.out
    mv extractedmin start
    (time /home/wales/bin/A9OPTIM.4.0) >& OPTIM.$count
    cp min.data.info min.data.info.$count
    head -1 min.data.info >> min.data.check
    mv points.final points.final.$count
    @ count +=1
 
 end

CHARMM users: create script relax as follows:

 #!/bin/csh
 
 set count = 1
 
 while ($count < 621)
 
    echo NATOMS 3002 > pathdata
    echo COPYFILES input.crd >> pathdata
    echo CHARMM >> pathdata
    echo EXTRACTMIN $count >> pathdata
    /home/wales/bin/pathsample.2.1 >& pathsample.out
    (time /home/wales/bin/COPTIM.4.0.31_64) >& OPTIM.$count
    cp min.data.info min.data.info.$count
    head -1 min.data.info >> min.data.check
 
    @ count +=1
 
end

NOTE: some values in this script are relevant to my system, like NATOMS=3002, so you need to change it according to atom numbers of your system. The number of count is equal to number of minima in your database (number of lines in min.data file) therefore this value should be also changed.

5. submit this script to queue on cluster:

 #PBS -q s1
 
 cd $PBS_O_WORKDIR
 ./relax

When finished you get a set of min.data.info.* files with coordinates that are optimized using new potential (if you didn't forget to update the force field :)).

6. final step: creation new binary file points.min; you will need new pathdata file:

 READMIN min.data.info.all
 NATOMS        3002
 COPYOPTIM
 TEMPERATURE   0.592
 GEOMDIFFTOL   0.1
 EXEC /home/wales/bin/A9OPTIM.4.0
 PERMDIST
 TRIPLES
 STARTTRIPLES
 ADDTRIPLES

AMBER users: add to pathdata file these two lines:

 COPYFILES   perm.allow coords.inpcrd coords.prmtop min.in
 AMBER9

CHARMM users: add to pathdata file these two lines:

 COPYFILES   perm.allow input.crd
 CHARMM

File min.data.info.all contains all min.data.info.* files and you can use cat command to make it easily (as is shown in next step).

7. submit this script to the queue on cluster:

 #PBS -q t1
 
 cd $PBS_O_WORKDIR
 
 for i in `ls min.data.info.*`; do cat $i>> min.data.info.all; done
 /home/wales/bin/pathsample.2.1 >& pathsample2.out

That's all! Now you have new min.data and points.min files and the only thing you need to to care now is to check if your original endpoints are on proper positions in both files - usually on the first and second positions. If not, you need to edit both files as is described here.