List of output files for PATHSAMPLE
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???
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 -- 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 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.
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 -- 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.
stationary.points.pdb -- as for redopoints, 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 redopoints (i.e., finish to start)
--mp466 10:31, 8 July 2008 (BST)