Finding an initial path between two end points (minima)
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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...