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solvent_nvt_equil_test.namd
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solvent_nvt_equil_test.namd
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###################################################
# NVT EQUILIBRATION
###################################################
# INPUT
set temp 310.0
vdwGeometricSigma yes
parameters ../par_opls_aam.inp
parameters ../updated.prm
parameters ../reference.prm
parameters ../../toppar/par_all36m_prot.prm
parameters ../../toppar/par_all36_na.prm
parameters ../../toppar/par_all36_carb.prm
parameters ../../toppar/par_all36_lipid.prm
parameters ../../toppar/par_all36_cgenff.prm
#parameters ../../toppar/par_interface.prm
parameters ../../toppar/toppar_all36_nano_lig.str
parameters ../../toppar/toppar_all36_nanolig_patch.str
parameters ../../toppar/toppar_all36_synthetic_polymer.str
parameters ../../toppar/toppar_all36_synthetic_polymer_patch.str
parameters ../../toppar/toppar_all36_polymer_solvent.str
#parameters ../../toppar/toppar_water_ions.str
#parameters ../../toppar/toppar_dum_noble_gases.str
#parameters ../../toppar/toppar_ions_won.str
parameters ../../toppar/toppar_all36_prot_arg0.str
#parameters ../../toppar/toppar_all36_prot_c36m_d_aminoacids.str
parameters ../../toppar/toppar_all36_prot_fluoro_alkanes.str
parameters ../../toppar/toppar_all36_prot_heme.str
parameters ../../toppar/toppar_all36_prot_na_combined.str
parameters ../../toppar/toppar_all36_prot_retinol.str
parameters ../../toppar/toppar_all36_prot_modify_res.str
parameters ../../toppar/toppar_all36_na_nad_ppi.str
parameters ../../toppar/toppar_all36_na_rna_modified.str
parameters ../../toppar/toppar_all36_lipid_archaeal.str
#parameters ../../toppar/toppar_all36_lipid_bacterial.str
parameters ../../toppar/toppar_all36_lipid_cardiolipin.str
#parameters ../../toppar/toppar_all36_lipid_cholesterol.str
parameters ../../toppar/toppar_all36_lipid_dag.str
parameters ../../toppar/toppar_all36_lipid_inositol.str
parameters ../../toppar/toppar_all36_lipid_lps.str
parameters ../../toppar/toppar_all36_lipid_miscellaneous.str
parameters ../../toppar/toppar_all36_lipid_model.str
parameters ../../toppar/toppar_all36_lipid_prot.str
#parameters ../../toppar/toppar_all36_lipid_sphingo.str
#parameters ../../toppar/toppar_all36_lipid_yeast.str
parameters ../../toppar/toppar_all36_lipid_hmmm.str
parameters ../../toppar/toppar_all36_lipid_detergent.str
parameters ../../toppar/toppar_all36_lipid_ether.str
parameters ../../toppar/toppar_all36_carb_glycolipid.str
#parameters ../../toppar/toppar_all36_carb_glycopeptide.str
parameters ../../toppar/toppar_all36_carb_imlab.str
#parameters ../../toppar/toppar_all36_label_spin.str
#parameters ../../toppar/toppar_all36_label_fluorophore.str
parameters ../../toppar/toppar_water_ions.mod.str
#parameters ../../toppar/toppar_water_ions.str
#parameters top_all36_carb.rtf
#parameters top_all36_cgenff.rtf
#parameters top_all36_na.rtf
#parameters top_all36_prot.rtf
#parameters top-ign-cgenff.rtf
#parameters top_opls_aam.inp
#parameters toppar_all36_carb_glycopeptide.str
parameters ../updated.prm
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1.0
# TOPOLOGY
structure ionized.psf
# INITIAL CONDITIONS
coordinates ionized_solvent.pdb
temperature $temp
# OUTPUT FREQUENCIES
outputenergies 10
outputtiming 10
outputpressure 10
restartfreq 10
XSTFreq 10
dcdfreq 10
# OUTPUT AND RESTART
outputname nvt_equil
restartname nvt_equil
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 42.5 0 0
cellbasisvector2 0 40.8 0
cellbasisvector3 0 0 45
cellOrigin 7.7 4.8 20.6
# 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
alch on
alchType fep
alchFile ionized_solvent.fep
alchCol B
alchOutFile nvt_equil.fepout
alchOutFreq 10
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 5.0
alchDecouple off
alchEquilSteps 0
set numSteps 5000 ; # 0.5 ns
set numMinSteps 500
runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp