Finding an initial path between two end points (minima)

When using AMBER9

If you have got database of minima (stored in files points.min, min.data, and min.data.info) from BHINTERP run, see [here], you can run CONNECT to connect them or find transition states and more minima :)

To do this the simplest way is to place in the same directory file odata.connect, e.g.:

  REOPTIMISEENDPOINTS
  EDIFFTOL     1.0D-4
  GEOMDIFFTOL  0.1
  MAXERISE     1.0D-4 1.0D-2
  MAXSTEP      0.8
  TRAD         0.5
  MAXMAX       1.0
  BFGSCONV     1.0D-6
  STEPS        300
  BFGSSTEPS    1000
  MAXBFGS      0.8
  BFGSMIN      1.0D-6
  BFGSTS       500 20 200 0.01 100
  NEWCONNECT   2 4 3.0 30.0 30 5.0
  NEWNEB       5 600 0.1
  DIJKSTRA     EXP
  NOFRQS
  NOHESS
  PERMDIST
  DUMPALLPATHS
  AMBER9 start
  POINTS

From pathdata file you need to just remove or comment line with BHINTERP, e.g.:

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

Files: coords.inpcrd, coords.prmtop, min.in, start, finish, perm.allow should remain unchanged.

As in BHINTERP run, NOFRQS is useful for large system. For smaller one you can use...