Finding an initial path between two end points (minima)

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When using the OPTIM/AMBER interface


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
  CHECKCHIRALITY
  NOCISTRANS
  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, in this case no frequencies are calculated. For smaller systems one can use ENDHESS, or ENDHESS and ENDNUMHESS in the odata.connect or odata.bhinterp files. Remember: if NOFRQS is not set, and you are using the AMBER9 keyword instead of the NAB keyword, only numerical second derivatives are available, so ENDHESS means in fact ENDHESS and ENDNUMHESS. If you want analytical second derivatives, use NAB instead of AMBER9, AND bear in mind that NAB second derivatives will be rubbish for systems with continuous cutoffs (i.e. the keyword ifswitch is not passed over to the NAB routines, since the force shifting is not implemented there yet)!