progdyn.conf

#This is the configuration file for PROGDYN.  This file is read by progdynstarterHP and
# the awk programs proggenHP, prog1stpoint, prog2ndpoint, and progdynb.
#The programs won't read anything past the first blank line,
#and this file must end with a blank line. 
#The program has a number of default values but they are unlikely to be what you want.
#Do not delete lines - rather, comment out lines for unwanted options.
#The values here are read repeatedly and most can be changed in the middle of running jobs
#***The keywords are case sensitive.  The following keywords should always be defined:***
#***method, charge, multiplicity, memory, processors, title
#*** method --The following word is copied exactly to the gaussian input file.
method um06/6-31g(d,p)
#To do a nonstandard route, make nonstandard 1.  For normal calcs, use nonstandard 0 or else leave it out.
#Then make a file called "nonstandard" containing the nonstandard route with no extra lines.
nonstandard 0
# NMRoptions As is NMR=1 will add a section for an NMR calc at every NMRevery intervals.  If you want to combine the two use nonstandard
#NMRtype 1
#NMRmethod B3LYP/cc-pvtz
#NMRevery 4
#geometry linear
rotationmode 1
#*** method2 --The options here are restricted, unrestricted, and read. restricted is the default
#If the method is U..., put unrestricted here and the .com files will have in them guess=mix.
#If you put read here, the .com files will contain guess=tcheck, which sometimes makes things faster, sometimes not.
#The use of read requires a specifically defined checkpoint file name using the keyword checkpoint.
method2 unrestricted 
charge 0
multiplicity 1
processors 12
#*** memory --The following "word" is copied exactly to the gaussian input file after %mem=.
memory 12gb
#*** killcheck and checkpoint -- You can use a specifically defined checkpoint file name by putting
#the name after the keyword checkpoint.  This is necessary if you use the read option with method2.
#Defined checkpoint names are an unnecessary modest hastle and if you do not want to bother, use killcheck 1
killcheck 1
#checkpoint g09.chk 
#*** diagnostics -- 0 prints out nothing extra, 1 (default) prints out extra stuff to a 
#file "diagnostics", 2 adds more stuff, 3 adds velocities to a file "vellist"
#4 adds the apparent temperature to vellist, but this is meaningless with quasiclassical calculations
diagnostics 0 
#*** title -- the title keyword must be followed by exactly four words
title j j j Methane
#*** initialdis -- 0 (default) turns off displacement of the normal modes, so that all trajectories start from the same place
# and only the energies and signs of the motion in the modes are randomized
# 1 gives a flat distribution of displacements where all of the possible values are equally likely
# 2 (recommended) gives a QM-like gaussian distribution of displacements, so that displacements in the middle are more likely that
# those at the end by 1/e
initialdis 2
#*** timestep -- this is the time between points in the trajectory.  Typical values would be 1E-15 or 0.5E-15 or 0.25E-15
timestep 1E-15
#*** scaling -- this lets you scale the gaussian frequencies by a constant 
scaling 1.0
temperature 553.15
#*** method3, method4, method5, and method6 -- These keywords let you add extra lines to the gaussian input file.
#method3 and method4 add lines at the top of the input after the lines defining the method, and 
#this is useful to implement things like the iop for mPW1k
#method5 and method6 add lines after the geometry, after a blank line of course
#only a single term with no spaces can be added, one per method line.  Here are some examples to uncomment if needed
#method4 IOp(3/76=0572004280)
method3 scrf=(smd,read)
#add the line below with big structures to get it to put out the distance matrix and the input orientation
#method3 iop(2/9=2000)
#method4 iop(3/124=3)
method5 eps=8.42
method6 rsolv=2.479
#*** methodfile -- This keyword lets you add more complicated endings to gaussian input files
#such as a gen basis set.  Put after the keyword the number of lines in a file you create called
#methodfile that contains the test you want to add to the end of the gaussian input
methodfile 0
#*** numimag --This tells the program the number of imaginary frequencies in the starting structure.
#if 0, treats as ground state and direction of all modes is random
#if 1, motion along the reaction coordinate will start out in the direction defined by searchdir
#if 2, only lowest freq will go direction of searchdir and other imag mode will go in random direction
numimag 0
#*** searchdir -- This keyword says what direction to follow the mode associated with the imaginary frequency.
#The choices are "negative" and "positive".  Positive moves in the direction defined in the gaussian frequency calculation
#for the imaginary frequency, while negative moves in the opposite direction.  The correct choice can be made either
#by a careful inspection of the normal modes and standard orientation geometry, or by trial and error.
searchdir positive
#*** classical --  for quassiclassical dynamics, the default, use 0.  for classical dynamics, use 1
#if there are no normal modes and the velocities are to be generated from scratch, use classical 2
classical 0
#*** DRP, saddlepoint, and maxAtomMove --to run a DRP use 'DRP 1' in the line below, otherwise leave it at 0 or comment it out
#the treatment of starting saddlepoints is not yet implemented so use saddlepoint no
#if DRP shows oscillations then decrease maxAtomMove
#DRP 1
#saddlepoint no
#maxAtomMove 0.01
#*** cannonball -- The program can "fire" a trajectory from a starting position toward a particular target, such as toward
#a ts.  To use this, make a file cannontraj with numAtom lines and three numbers per line that defines the vector
#for firing the trajectory, relative to the starting geometry's standard orientation.  The number following cannonball sets 
#the extra energy being put into the structure in kcal/mol
#cannonball 10
#*** keepevery --This tells the program how often to write the gaussian output file to file dyn, after the first two points.
#Use 1 for most dynamics to start with, but use a higher number to save on disk space or molden loading time.
keepevery 1
#*** highlevel --For ONIOM jobs, the following line states the number of highlevel atoms, 
#which must come before the medium level atoms.  Use some high value such as 999 if not using ONIOM
highlevel 999
#*** fixedatom1, fixedatom2, fixedatom3, and fixedatom4 - These fix atoms in space.
#Fixing one atom serves no useful purpose and messes things up, while fixing two atoms 
#fixes one distance and fixing three has the effect of fixing three distances, not just two
#in current form fixed atoms only are meant to work with no displacements, that is, initialdis=0
#fixedatom1 2
#fixedatom2 3
#fixedatom3 19
#*** boxon and boxsize - With boxon 1, a cubic box is set such that atoms that reach the edge 
#are reflected back toward the middle.  Useful for dynamics with solvent molecules.  This is a crude 
#implementation that is ok for a few thousand femtoseconds but will not conserve energy long term.
#Set the box size so as to fit the entire initial molecule but not have too much extra room.  
#The dimensions of the box are two times the boxsize, e.g. boxsize 7.5 leads to a box that is 15 x 15 x 15 angstroms
boxon 0
boxsize 7.5
#*** displacements -- This keyword lets you set the initialdis of particular modes by using a series of lines of the format
# displacements NumberOfMode InitialDisForThatMode, as in the example below. You should be able to do as many of these as you like
# you might consider this for rotations where a straight-line displacement goes wrong at large displacements
# The choices for InitialDisForThatMode are 0, 1, 2, and 10, where 10 does the same thing as 0 but is maintained for now because
# a previous version of the program had a bug that made 0 not work.  
#displacements 2 0
#displacements 3 0
#*** etolerance --This sets the allowable difference between the desired energy in a trajectory and the actual
#energy, known after point 1 from the potential energy + the kinetic energy in the initial velocities.
#The unit is kcal/mol and 1 is a normal value for mid-sized organic systems.  For very large and floppy molecules, a larger value 
#may be needed, but the value must stay way below the average thermal energy in the molecule (not counting zpe).  
#If initialdis is not 0 and few trajectories are being rejected, decrease the value.
etolerance 1
#*** controlphase --It is sometimes useful to set the phase of particular modes in the initialization of trajectories. 
#The format is controlphase numberOfModeToControl positive or controlphase numberOfModeToControl negative.
#controlphase 2 positive
#*** damping -- The damping keyword lets you add or subtract energy from the system at each point, by multiplying the velocities
#by the damping factor.  A damping of 1 has no effect, and since you mostly want to change the energy slowly, normal values range
#from 0.95 to 1.05.  The use of damping lets one do simulated annealing - you add energy until the structure is moving enough
#to sample the kinds of possibilities you are interested in, then you take away the energy slowly.  
damping 1
#*** reversetraj --This keyword sets the trajectories so that both directions from a transition state are explored.
reversetraj true


#updated Aug 9, 2007 to include the possibility of classical dynamics by the keyword classical
#updated Jan 2008 to include fixed atoms, ONIOM jobs, keepevery, and box size
#update Feb 2008 to include methodfile parameter
# updated Nov 2008 to allow for start without an initial freq calc using classical = 2
# update Aug 2010 to include etolerance, damping controlphase and reversetraj