Finding an initial path between two end points (minima)
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 COMMENT JOBSPERNODE 1 PBS 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)!