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 (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)