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complex_md_backward_test.namd
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###################################################
# MD BACKWARD
###################################################
# INPUT
set temp 310.0
vdwGeometricSigma yes
parameters ../par_opls_aam.inp
parameters ../updated.prm
parameters ../reference.prm
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1.0
# TOPOLOGY
structure ionized.psf
# INITIAL CONDITIONS
coordinates ionized_complex.pdb
bincoordinates md_forward_2.coor
binvelocities md_forward_2.vel
extendedsystem md_forward_2.xsc
# OUTPUT FREQUENCIES
outputenergies 10
outputtiming 10
outputpressure 10
restartfreq 10
XSTFreq 10
dcdfreq 10
# OUTPUT AND RESTART
outputname md_backward_modi
restartname md_backward_modi
binaryoutput yes
binaryrestart yes
# CONSTANT-T
langevin on
langevinTemp $temp
langevinDamping 1.0
# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSpacing 1.0
# Periodic Boundary Conditions
# cellBasisVector1 30.0 0 0
# cellBasisVector2 0 30.0 0
# cellBasisVector3 0 0 30.0
# cellOrigin 0.0 0.0 0.0
# WRAP WATER FOR OUTPUT
wrapAll on
wrapWater on
# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 100
LangevinPistonDecay 50
LangevinPistonTemp $temp
StrainRate 0.0 0.0 0.0
useGroupPressure yes
useFlexibleCell no
# SPACE PARTITIONING
stepspercycle 10
margin 1.0
# CUT-OFFS
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0
# RESPA PROPAGATOR
timestep 2.0
fullElectFrequency 2
nonbondedFreq 1
# SHAKE
rigidbonds all
rigidtolerance 0.000001
rigiditerations 400
# COM
ComMotion no
# FEP PARAMETERS
# source ../../fep.tcl
source ../fep.tcl
alch on
alchType fep
alchFile ionized_complex.fep
alchCol B
alchOutFile md_backward_modi.fepout
alchOutFreq 10
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 5.0
alchDecouple off
#alchEquilSteps 500000
#alchLambda 0.9375
#alchLambda2 0.875
#run 5000000 ; # 5 ns
alchEquilSteps 50
set numSteps 500 ; # 0.5 ns as a total
runFEP 1.0 0.0 -0.0625 $numSteps