List of output files for PATHSAMPLE

Input Structures

start.<n> -- input coordinate files for OPTIM generated via pathsample

input.crd.<n> -- input coordinate files for COPTIM (version of OPTIM that works with CHARMM) generated via pathsample

finish.<n> -- input coordinate files for OPTIM generated via pathsample

Input files that should be provided to a pathsample job

pathdata -- keywords file for pathsample

pathdata.change -- 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

odata.new.<n> -- files generated by OPTIM for restarting from that point (path calculations?)

odata.<n> -- OPTIM input file created by pathsample

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

path.info.data.<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 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.A, min.B -- files detailing the membership of the A and B states. Each contains the number of minima in the state, followed by the indices of the minima in the 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.

[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

points.min, points.ts -- unformatted direct access file versions of min.data and ts.data, with the stationary points in the same order.

path.<n>.xyz -- path coordinates for path <n> in Xmakemol format produced with debugging on

path.xyz -- total path coordinates in Xmakemol format produced with debugging on

energies -- ?????

Misc

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

commit.data -- committor probabilities for the minima

pairs.data -- record of connection attempts already performed

min.done -- record of minima from UNTRAP runs

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.

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 redopoints (i.e., finish to start)

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