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 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 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

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

min.data.info.<n> -- coordinate input files for input minima created by OPTIM for PATHSAMPLE

path.info.data.<n> -- min.ts.min triple with frequencies, and structures created by OPTIM for PATHSAMPLE

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

Output

OPTIM.connect.<n> -- output from OPTIM runs

min.A, min.B and min.data -- A, B and intermediate minima, respectively

ts.data -- transition states

<file>.fastest -- GT data for the fastest connection of the database

<file>.regrouped -- data after regrouping into free energy groups

<file>.retained -- stationary point data retained after pruning via RETAINSP keyword

<file>.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

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 completed

commit.data -- committor probabilities for the minima

pairs.data -- record of connection attempts already performed

min.done -- record of minima from UNTRAP runs

redopoints -- ?????

extractedmin.crd -- ????

Epath -- ????

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