Difference between revisions of "Using BHINTERP to find minima between two end points"

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import>Em427
 
import>Em427
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'''When using AMBER9'''
  
'''When using AMBER9'''
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On the beginning you need to have two optimized structures which are called endpoints. Often they are the 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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What files do you need to find a path connecting both endpoints?
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1. coords.inpcrd -- file with coordinates in AMBER9 format (it can contain geometry of one of the endpoints)
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2. coords.prmtop -- AMBER9 topology file prepared according to information presented [Link here]
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3. min.in - file with AMBER9 keywords describing the conditions for molecular dynamics of the studied system, e.g.:
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Minimization
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&cntrl
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imin=1, maxcyc=1, ncyc=1,
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igb=2, saltcon=0.2,
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ntx=1, ntb=0,
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cut=15.0, rgbmax=12.0, ifswitch=1
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/
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4. ''start'' -- file with x, y, z coordinates of the first endpoint
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5. ''finish'' -- file with x, y, z coordinates of the second endpoint
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6. ''start.1'' which is a copy of ''start''
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7. ''finish.2'' -- a copy of ''finish''
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8. odata.bhinterp -- file with OPTIM keywords specifying method of searching of minima, convergence criterion, etc. e.g.:
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REOPTIMISEENDPOINTS
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MAXBFGS 1.0
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MAXERISE 1.0D-4
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EDIFFTOL 1.0D-6
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GEOMDIFFTOL 0.1
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BFGSMIN 1.0D-6
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BFGSSTEPS 60000
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NOFRQS
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DUMPDATA
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AMBER9 start
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POINTS
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These particular keywords are chosen for large system, a few thousands atoms where calculation of frequencies is too time consuming. For smaller system you can use

Revision as of 21:44, 30 April 2008

When using AMBER9


On the beginning you need to have two optimized structures which are called endpoints. Often they are the 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.: 

  REOPTIMISEENDPOINTS
  MAXBFGS  1.0
  MAXERISE 1.0D-4
  EDIFFTOL 1.0D-6
  GEOMDIFFTOL 0.1
  BFGSMIN  1.0D-6
  BFGSSTEPS 60000
  NOFRQS
  DUMPDATA
  AMBER9 start
  POINTS

These particular keywords are chosen for large system, a few thousands atoms where calculation of frequencies is too time consuming. For smaller system you can use

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