Difference between revisions of "Using BHINTERP to find minima between two end points"
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− | On the beginning you need to have two optimized structures which are called endpoints. Often they are |
+ | 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). |
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COPYOPTIM |
COPYOPTIM |
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COPYFILES perm.allow min.in coords.inpcrd coords.prmtop |
COPYFILES perm.allow min.in coords.inpcrd coords.prmtop |
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− | COMMENT thresh maxe BHsteps RMS T |
+ | 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 |
BHINTERP 5 -9100.0 1 0.01 1.00 0.4 0.5 10.0 0.5 |
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AMBER9 |
AMBER9 |
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− | Take care to change path to executable, NATOMS and maxe (the second parameter in BHINTERP, it should/can be about 200 smaller than energies of both endpoints). Line 'JOBSPERNODE 1' is necessary for parallel jobs. Usage of PERMDIST requires file ''perm.allow'' in the same directory. |
+ | Take care to change path to executable file, values of NATOMS and maxe (the second parameter in BHINTERP, it should/can be about 200 smaller than energies of both endpoints). Line 'JOBSPERNODE 1' is necessary for parallel jobs. Usage of PERMDIST requires file ''perm.allow'' in the same directory. |
10. ''perm.allow'' -- file with list of atoms that may be permuted. Information how to get this file you can find [[Link here]]. |
10. ''perm.allow'' -- file with list of atoms that may be permuted. Information how to get this file you can find [[Link here]]. |
Revision as of 09:36, 1 May 2008
When using AMBER9
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)
2. coords.prmtop -- AMBER9 topology file prepared according to information presented [Link here]
3. min.in - file with AMBER9 keywords describing the conditions for molecular dynamics of the studied system, 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
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.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 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 ...
9. pathdata -- in this file all necessary PATHSAMPLE keywords should be put:
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 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 AMBER9
Take care to change path to executable file, values of NATOMS and maxe (the second parameter in BHINTERP, it should/can be about 200 smaller than energies of both endpoints). Line 'JOBSPERNODE 1' is necessary for parallel jobs. Usage of PERMDIST requires file perm.allow in the same directory.
10. perm.allow -- file with list of atoms that may be permuted. Information how to get this file you can find Link here.