Difference between revisions of "List of output files for PATHSAMPLE"

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import>Jmc49
import>Mp466
 
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odata.<n> -- OPTIM input file
  
odata.<n> -- OPTIM input file
   
−
odata.new.<n> -- files generated by OPTIM for restarting from that point???
 +
odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM)
   
 
'''Input files that might be provided for a pathsample job'''
 
'''Input files that might be provided for a pathsample job'''
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OPTIM.connect.<n> -- output from OPTIM connection-making runs (only kept if COPYOPTIM keyword is present in pathdata)
  
OPTIM.connect.<n> -- output from OPTIM connection-making runs (only kept if COPYOPTIM keyword is present in pathdata)
   
−
min.data -- file containing info on all the minima in the database. One line per minimum; the line number is the index of that minimum. Each line stores the potential energy, the logarithm of the product of positive mass-weighted Hessian eigenvalues, the order of the point group, the three eigenvalues of the inertia tensor, and (optionally) an order parameter.
 +
min.data -- info on all the minima in the database. One line per minimum; the line number is the index of that minimum. Each line stores the potential energy, the logarithm of the product of positive mass-weighted Hessian eigenvalues, the order of the point group, the three eigenvalues of the inertia tensor, and (optionally) an order parameter.
−  
⚫
min.A, min.B -- files detailing the membership of the A and B states. Each contains the number of minima in that state, followed by the indices of the minima in that state (one per line).
 
   
 
ts.data -- like min.data but for the transition states. Contains additional info on the connectivity of the TS: two columns for the indices of the connected minima, between the order of the point group and the inertia tensor stuff. No order parameter column.
  
ts.data -- like min.data but for the transition states. Contains additional info on the connectivity of the TS: two columns for the indices of the connected minima, between the order of the point group and the inertia tensor stuff. No order parameter column.
  +
  +
min.A, min.B -- details the membership of the A and B states. During the initial path calculation
  ⚫
the endpoints are defined by these indices. Each contains the number of minima in that state, followed by the indices of the minima in that state (one per line).
   
 
points.min, points.ts -- unformatted direct access file storing coordinates of the stationary points listed in min.data and ts.data, in the same order.
  
points.min, points.ts -- unformatted direct access file storing coordinates of the stationary points listed in min.data and ts.data, in the same order.
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ts.attempts -- records TS where short cut paths have already been attempted
  
ts.attempts -- records TS where short cut paths have already been attempted
   
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commit.data -- committor probabilities for the minima
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commit.data -- committer probabilities for the minima
   
 
pairs.data -- record of connection attempts already performed
  
pairs.data -- record of connection attempts already performed
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min.done -- record of minima from UNTRAP runs
  
min.done -- record of minima from UNTRAP runs
   
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redopoints -- coordinates of the stationary points on the fastest path found with a Dijkstra analysis, in reverse order (finish to start). 'points'-style xyz format.
 +
redopoints -- Contrary to what is printed in the output file (!!!), coordinates of the transition states (only) on the fastest path found with a Dijkstra analysis, in reverse order (finish to start). 'points'-style xyz format.
   
−
stationary.points.pdb -- as for redopoints, but in PDB format for proteins, for CHARMM.
 +
stationary.points.pdb -- minima and transition states on the fastest path, in reverse order but in PDB format for proteins. For CHARMM.
   
 
extractedmin.crd -- charmm-formatted coordinates of a minimum extracted from the database using EXTRACTMIN <index> keyword
  
extractedmin.crd -- charmm-formatted coordinates of a minimum extracted from the database using EXTRACTMIN <index> keyword
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extractedts -- plain xyz coordinates of a TS extracted from the database using EXTRACTTS <index> keyword
  
extractedts -- plain xyz coordinates of a TS extracted from the database using EXTRACTTS <index> keyword
   
−
Epath -- Energies of the stationary points on the fastest path from a Dijkstra analysis, as a numbered list in the same order as redopoints (i.e., finish to start)
 +
Epath -- Energies of the stationary points on the fastest path from a Dijkstra analysis, as a numbered list in the same order as stationary.points.pdb (i.e., finish to start)
   
 
--[[User:mp466|mp466]] 10:31, 8 July 2008 (BST)
  
--[[User:mp466|mp466]] 10:31, 8 July 2008 (BST)

Latest revision as of 22:41, 17 November 2008

Files PATHSAMPLE creates for input to OPTIM

start.<n> -- coordinate files for the start minima in OPTIM connection-making runs (AMBER and AMH varieties)

input.crd.<n> -- coordinate files for the start minima in COPTIM connection-making runs (CHARMM variety)

finish.<n> -- coordinate files for the end minima in OPTIM connection-making runs (all varieties)

odata.<n> -- OPTIM input file

odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM)

Input files that might be provided for a pathsample job

pathdata -- keywords file for pathsample

pathdata.change -- (optional) file read in during pathsample run to change parameters whilst the job is running

odata.start -- OPTIM data file for initial minimization and frequency calc for start file (initial minimum in the start [A or B] state)

start.crd or AMHstart -- coordinates in CHARMM or AMH format, respectively, for the initial start-state minimum

odata.finish -- OPTIM data file for initial minimization and frequency calc for finish file (initial minimum in the finish [B or A] state)

finish.crd or AMHfinish -- coordinates in CHARMM or AMH format, respectively, for the initial finish-state minimum

odata.connect -- OPTIM data file for CONNECT run

min.data.info.<n> -- min.data-style (plus coordinates) input files for minima, created by OPTIM for PATHSAMPLE

path.info.<n> -- min.ts.min triples with mass-weighted Hessian eigenvalues and structures, created by OPTIM for PATHSAMPLE

nodes.info -- processor addresses for a distributed memory machine

path.info.startup -- an OPTIM path.info file from a connect run that connects an A minimum to a B minimum. Used if the initial connected path is created by a single OPTIM job without pathsample. Use in conjunction with pathsample keywords STARTFROMPATH or ADDPATH.

Output

OPTIM.connect.<n> -- output from OPTIM connection-making runs (only kept if COPYOPTIM keyword is present in pathdata)

min.data -- info on all the minima in the database. One line per minimum; the line number is the index of that minimum. Each line stores the potential energy, the logarithm of the product of positive mass-weighted Hessian eigenvalues, the order of the point group, the three eigenvalues of the inertia tensor, and (optionally) an order parameter.

ts.data -- like min.data but for the transition states. Contains additional info on the connectivity of the TS: two columns for the indices of the connected minima, between the order of the point group and the inertia tensor stuff. No order parameter column.

min.A, min.B -- details the membership of the A and B states. During the initial path calculation the endpoints are defined by these indices. Each contains the number of minima in that state, followed by the indices of the minima in that state (one per line).

points.min, points.ts -- unformatted direct access file storing coordinates of the stationary points listed in min.data and ts.data, in the same order.

[min.data,min.A,min.B,ts.data,points.min,points.ts].fastest -- database containing only the stationary points on the fastest connection of the database (found using a Dijkstra rate-constant analysis.)

[min.data,min.A,min.B,ts.data,points.min,points.ts].regrouped -- database after grouping into free energy groups

[min.data,min.A,min.B,ts.data,points.min,points.ts].retained -- stationary point data retained after pruning via RETAINSP keyword

[min.data,min.A,min.B,ts.data,points.min,points.ts].removed -- stationary point data retained after pruning via REMOVESP keyword

Misc

ts.attempts -- records TS where short cut paths have already been attempted

commit.data -- committer probabilities for the minima

pairs.data -- record of connection attempts already performed

min.done -- record of minima from UNTRAP runs

redopoints -- Contrary to what is printed in the output file (!!!), coordinates of the transition states (only) on the fastest path found with a Dijkstra analysis, in reverse order (finish to start). 'points'-style xyz format.

stationary.points.pdb -- minima and transition states on the fastest path, in reverse order but in PDB format for proteins. For CHARMM.

extractedmin.crd -- charmm-formatted coordinates of a minimum extracted from the database using EXTRACTMIN <index> keyword

extractedmin -- plain 'points'-style xyz coordinates of a minimum extracted from the database using EXTRACTMIN <index> keyword

extractedts.crd -- charmm-formatted coordinates of a TS extracted from the database using EXTRACTTS <index> keyword

extractedts -- plain xyz coordinates of a TS extracted from the database using EXTRACTTS <index> keyword

Epath -- Energies of the stationary points on the fastest path from a Dijkstra analysis, as a numbered list in the same order as stationary.points.pdb (i.e., finish to start)

--mp466 10:31, 8 July 2008 (BST)

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