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