Relaxing existing minima with new potential and creating new database

Sometimes 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:

1. create subdirectory relax_min

2. copy points.min, min.data, odata.start, perm.allow to relax_min

-- AMBER users: copy also coords.prmtop, coords.inpcrd, min.in

-- CHARMM users: copy also input.crd

3. change name of odata.start into odata

4. AMBER users: create script relax as follows:

 #!/bin/csh
 set count = 1
 
 while ($count < 621)
 
    echo NATOMS 3002 > pathdata
    echo AMBER9 >> pathdata
    echo EXTRACTMIN $count >> pathdata
    /home/em427/bin/pathsample.2.1 >& pathsample.out
    mv extractedmin start
    (time /home/em427/bin/A9OPTIM.4.0) >& OPTIM.$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: instead of line:

    echo AMBER9 >> pathdata

use:

    echo CHARMM >> pathdata

NOTE: some values in this script are relevant to my system like NATOMS=3002, 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 non-blank lines in min.data file) therefore this value should be also changed.

5. submit this script to queue using e.g. the following script

 #PBS -N Cdd-Ddd-0
 #PBS -q h16
 #PBS -l nodes=16
 
 cd $PBS_O_WORKDIR
 ./relax