Input file example
# add a # charater to comment a line
#RunType = Energy, Optimization, MD, MDConfo, REMDConfo, PIMD
RunType=MD
#OptimizerType=External
#Model = MM , Mopac , Orca or FireFly, Gaussian, ...
Model=MM
QMKeys=PM3
#addH4Corrections=TRUE
#addD3Corrections=TRUE
mopacCommand=/home/allouche/Softwares/MOPAC2009/MOPAC2009.exe
orcaCommand=orca
fireflyCommand=firefly
#Confo
gaussianCommand=g03
fireflyCommand=firefly
numberOfGeometries=3
tolEnergy=0.1
tolDistance=0.1
ConfoOptMM=TRUE
#ConfoOptMopac=TRUE
ConfoOptMopacMethod=PM6 GNORM=0.001
ConfoOptFireFly=FALSE
# remove # if post processing required
#mopacKeywordsPost=PM6
gaussianKeywordsPost=B3LYP/aug-cc-pvdz
lascmdKeywordsPost=B3LYP/aug-cc-pvdz
orcaKeywordsPost=AM1 Opt
fireflyKeywordsPost=GBASIS=PM3
mopacKeywordsPost=PM6
#fireflyKeywordsPost=AM1
#MM
# AMBER, UFF(not implemented), PAIRWISE
ForceFieldType=0
ForceFieldUseBond=TRUE
ForceFieldUseBend=TRUE
ForceFieldUseDihedral=TRUE
ForceFieldUseImproper=FALSE
ForceFieldUseNonBonded=TRUE
ForceFieldUseHydrogenBonded=FALSE
ForceFieldUsecoulomb=TRUE
ForceFieldUseVanderWals=TRUE
# NOCONSTRAINTS = 0, BONDSCONSTRAINTS = 1, BONDSANGLESCONSTRAINTS = 2
Constraints=0
#MD
updateFrequency=1
#Time in ps
heatTime = 0.0
equiTime = 50.0
runTime = 50.
coolTime = 0
timeExchange = 1.0
heatTemp = 0
runTemp = 3
runTempMax = 300
nTemperatures = 10
#in fs
stepSize = 0.5
# VERLET = 0, BEEMAN = 1, STOCHASTIC = 2, LANGEVIN = 3, QTB = 4
integrator = 4
# NONE = 0, ANDERSEN = 1, BERENDSEN = 2, BUSSI = 3, NH = 4
thermostat = 0
friction=40
collide = 20
# NONE = 0, LANGEVIN = 1
#PIMDThermostat = 1
# NONE = 0, STAGING = 1, NORMALMODE=2
#PIMDTransformation = 2
#QuasiNewton
quasiNewtonMaxIterations = 2000
quasiNewtonUpdateFrequency = 1
quasiNewtonEpsilon = 0.001
quasiNewtonTolerence = 1e-16
quasiNewtonMaxLines = 25
#ConjugateGradient
conjugateGradientGradientNorm = 1e-3
conjugateGradientMaxIterations = 100
conjugateGradientUpdateFrequency = 1
conjugateGradientMaxLines = 25
conjugateGradientInitialStep = 0.001
# 1 : Hestenes Stiefel, 2 : Fletcher Reeves, 3 : Polak Ribiere, 4 : Wolf Powell
conjugateGradientMethod = 1
# a template input file can be created by Gabedit for any geometry
#Geometry, nAtoms, charge, spin multiplicity. For each atom : symbol, MMType, pdbType, residueName, numResidue, charge, layer, x(Ang),y,z, nconn, num1, type1, num2, type2,...
Geometry
2 0 1
C CA CA HOH 1 0.000000 2 1 0.000000 0.0000 0.700000 1 2 1
C CA CA HOH 1 0.000000 2 1 0.000000 0.000000 -0.700000 1 1 1