View source for Using BHINTERP to find minima between two end points

'''When using [[AMBER]]'''


On the beginning you need to have two optimized structures which are called endpoints. Often they are initial and final structures of studied path or reaction (however, here ''reaction'' means geometrical change in the system, not breaking and forming new bonds).


What files do you need to find a path connecting both endpoints?

1. ''coords.inpcrd'' -- file with coordinates in AMBER9 format (it can contain geometry of one of the endpoints, no matter which one)

2. ''coords.prmtop'' -- AMBER9 topology file prepared according to information presented [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here], while some very useful tutorials how to get topology file are presented [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/AMBER here]

3. ''min.in'' - file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (but with only one cycle, just to calculate the energy), e.g.:

  Minimization
  &cntrl
     imin=1, maxcyc=1, ncyc=1,
     igb=2, saltcon=0.2,
     ntx=1, ntb=0,
     cut=15.0, rgbmax=12.0, ifswitch=1
   /

4. ''start'' -- file with x, y, z coordinates of the first endpoint (just plain numbers, without atom names or types as is in xyz format!)

5. ''finish'' -- file with x, y, z coordinates of the second endpoint

6. ''start.1'' which is a copy of ''start''

7. ''finish.2'' -- a copy of ''finish''

8. ''odata.start'' -- file with keywords for optimizing ''start'' file, eg.:

   EDIFFTOL    1.0D-6
   GEOMDIFFTOL 0.1
   BFGSMIN     1.0D-6
   MAXERISE    1.0D-4 1.0D-2
   BFGSSTEPS   1000
   MAXBFGS     0.3
   DUMPDATA
   NOFRQS
   AMBER9 start
   POINTS

9. ''odata.finish'' -- file with keywords for optimizing ''finish'' file, e.g.:

   EDIFFTOL    1.0D-6
   GEOMDIFFTOL 0.1
   BFGSMIN     1.0D-6
   MAXERISE    1.0D-4 1.0D-2
   BFGSSTEPS   1000
   MAXBFGS     0.3
   DUMPDATA
   NOFRQS
   AMBER9 finish
   POINTS

10. ''odata.bhinterp'' -- file with OPTIM keywords specifying method of searching of minima, convergence criterion, etc. e.g.:

   MAXBFGS     1.0
   MAXERISE    1.0D-4
   EDIFFTOL    1.0D-6
   GEOMDIFFTOL 0.1
   BFGSMIN     1.0D-6
   BFGSSTEPS   10000
   NOFRQS
   DUMPDATA
   PERMDIST
   CHECKCHIRALITY
   NOCISTRANS
   AMBER9 start
   POINTS

NOFRQS is specially useful for large system, a few thousands atoms, where calculation of frequencies is too time consuming. For smaller system you can use ENDHESS or ENDNUMHESS or NOHESS or...

11. ''pathdata'' -- in this file all necessary PATHSAMPLE keywords should be put:

   EXEC /home/wales/bin/A9OPTIM.4.0
   TEMPERATURE 0.592
   NATOMS      2923
   COMMENT TRIPLES
   COMMENT ADDTRIPLES
   COMMENT JOBSPERNODE 1
   PBS
   CYCLES      1000
   ITOL        1.0D0
   GEOMDIFFTOL 0.1
   EDIFFTOL    1.0D-6
   PERMDIST
   DIJINITSTART EXP
   COPYOPTIM
   COPYFILES perm.allow min.in coords.inpcrd coords.prmtop
   COMMENT  thresh  maxe     BHsteps    RMS   T    step-size accrat   K   sfrac
   BHINTERP    5   -9100.0      1      0.01  1.00    0.4      0.5   10.0   0.5
   CHECKCHIRALITY
   NOCISTRANS
   AMBER9

Take care to change path to executable file (if necessary), values of NATOMS and maxe (the second parameter in BHINTERP, it should/can be about 200 smaller than energies of both endpoints). Line 'PBS' is necessary for parallel jobs, however you can also use CPUS. Usage of PERMDIST requires file ''perm.allow'' in the same directory.

12. ''perm.allow'' -- file with list of atoms that may be permuted. Information how to get this file you can find [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-pdb.py here].


'''How to restart job?'''

If you have some minima stored in ''points.min'' file and you would like to increase their number, change 'DIJINITSTART EXP' into 'DIJINITCONT EXP'. That allows you to continue searching for minima. But if you restart your job with 'DIJINITSTART EXP' - you lost all minima you have found before, because file ''points.min'' will be overwrite! '''Update''': new version of [[PATHSAMPLE]] does not overwrite this file, just stops with warning.