; VARIOUS PREPROCESSING OPTIONS
title = Colicin_A_10h_md,reaction field
cpp = /lib/cpp
include =
;define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.004
nsteps = 250000 ; 1ns
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000000
nstvout = 1000000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 50000
; Output frequency for energies to log file and energy file
nstlog = 50000
nstenergy = 50000
; Output frequency and precision for xtc file
nstxtcout = 50000
xtc-precision = 500000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = system
; Selection of energy groups
energygrps = POPC_PII SOL
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 3 ; nstlist * dt should = approx 10fs
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.8
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = reaction-field
rcoulomb-switch = 0
rcoulomb = 1.4 ; this was 1.8 (wrong) in prev simulations
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-rf = 78.5
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = POPC_PII_NA+_CL- SOL
; Time constant (ps) and reference temperature (K)
tau-t = 0.1 0.1
ref-t = 310 310
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 4 4
compressibility = 4.5e-5 4.5e-5
ref-p = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed = 343401
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen-temp = 310
gen-seed = 5521904
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no