# GENERATED BY CHARMM-GUI (http://www.charmm-gui.org) v3.7 on Feb, 10. 2025. JOBID=3918698540
# NAMD SIMULATION OPTION for FEP/REMD
structure complex.psf
coordinates complex.pdb
# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type parameter file(s)
# multiple definitions may be used but only one file per definition
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_moreions.str
parameters ../../toppar/toppar_all36_nano_lig.str
parameters ../../toppar/toppar_all36_nano_lig_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/cam.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_model.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_sphingo.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_lnp.str
parameters ../../toppar/toppar_all36_lipid_lps.str
parameters ../../toppar/toppar_all36_lipid_mycobacterial.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_tag.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_lipid_oxidized.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 ../morph.prm # Custom topology and parameter files for Morph
# PME (for full-system periodic electrostatics)
PME yes;
PMEGridSpacing 1.0;
wrapAll on; # wrap other molecules too
langevin on
langevinDamping 1.0
langevinTemp 310
# constant pressure
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100.0
langevinPistonDecay 100.0
langevinPistonTemp 310
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
# 1-2: all atoms pairs that are bonded are going to be ignored
# 1-3: 3 consecutively bonded are excluded
# scaled1-4: include all the 1-3, and modified 1-4 interactions
# electrostatic scaled by 1-4scaling factor 1.0
# vdW special 1-4 parameters in charmm parameter file.
1-4scaling 1.0
switching on # switching is used for vdW forces.
# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
# switchdist - where you start to switch
# cutoff - where you stop accounting for nonbond interactions.
# correspondence in charmm:
# (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
pairlistdist 13.5; # stores the all the pairs with in the distance it should be larger
# than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
rigidBonds all; # Bound constraint all bonds involving H are fixed in length
# Integrator Parameters
timestep 2.0; # fs/step
#fullElectFrequency 2; # PME every step
#nonbondedFreq 1; # nonbonded forces every step
commotion no;
alch on
singleTopology on
sdBondScaling off # Shobana terms disabled
#unperturbedBondFile ../unpert.info
alchEnsembleAvg off
alchType FEP
alchFile complex.pdb
alchCol B
alchOutFreq 100
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 6.0
alchDecouple off
alchEquilSteps 0