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complex.conf
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#############################################################
## JOB DESCRIPTION ##
#############################################################
# Eq. of KcsA
# embedded in POPC membrane, ions and water.
# Protein released. PME, Constant Pressure/Area.
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure complex.psf
coordinates complex.pdb
outputName complex
set temperature 310
# Continuing a job from the restart files
if {0} {
set inputname LRRK2-VB12-out1
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.restart.xsc
}
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
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_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/jz4.prm # Custom topology and parameter files for JZ4
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 98. 0. 0.
cellBasisVector2 0. 98. 0.
cellBasisVector3 0. 0. 96.
cellOrigin -0.0390621498227 -0.0503903478384 0.05063835904
}
# wrapWater on
wrapAll on
### gbsa
GBIS on
solventDielectric 78.5
ionConcentration 0.3
alphaCutoff 15
sasa on
surfaceTension 0.0072
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 16.
switching on
switchdist 15.
pairlistdist 18
# Integrator Parameters
timestep 1 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSizeX 81
PMEGridSizeY 81
PMEGridSizeZ 90
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
#restartfreq 10000 ;# 1000steps = every 2ps
#dcdfreq 10000
#xstFreq 10000
#outputEnergies 10000
#outputPressure 10000
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile nottails.fix.pdb
fixedAtomsCol B
fixedAtomsForces on
}
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
#eFieldOn yes
#eField 0 0 -0.155
#############################################################
## EXECUTION SCRIPT ##
#############################################################
set ts 0
coorfile open dcd complex.dcd
while {[coorfile read] != -1 } {
firstTimestep $ts
run 0
incr ts 1
}
coorfile close