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pullf1500.mdp
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pullf1500.mdp
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title = Pulling simulation
;define = -DPOSRES_NC
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ;
nstcomm = 10
; Output parameters
nstxout = 1000 ; every x ps
nstvout = 1000
nstfout = 1000
nstxtcout = 1000 ; every x ps
nstlog = 1000
nstenergy = 2000
; Bond parameters
constraint_algorithm = lincs
constraints = h-bonds
continuation = yes ; continuing from NPT
morse = yes ; Convert harmonic bonds to morse potentials
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = v-rescale
tc_grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; This selects the subset of atoms for the compressed
; trajectory file. You can select multiple groups. By
; default, all atoms will be written.
compressed-x-grps = Protein
; Selection of energy groups
energygrps = Protein
; COM PULLING
pull = yes
;pull-print-com = yes
pull-print-ref-value = yes
pull-print-components = yes
pull-nstxout = 10000
pull-nstfout = 10000
pull-ngroups = 6
pull-ncoords = 6
;parameters for all groups
pull-group1-name = 1_ACE_1
pull-group2-name = 1_NME_1
pull-group3-name = 1_ACE_2
pull-group4-name = 1_NME_2
pull-group5-name = 1_ACE_3
pull-group6-name = 1_NME_3
pull-coord1-type = constant-force
;pull-coord1-rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k = 1500
pull-coord1-geometry = direction
pull-coord1-groups = 0 2
pull-coord1-dim = N N Y
pull-coord1-vec = 0 0 1
pull-coord1-start = yes
;pull-coord1-origin = 0 0 0
pull-coord2-type = constant-force
;pull-coord2-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord2-k = -1500
pull-coord2-geometry = direction
pull-coord2-groups = 0 1
pull-coord2-dim = N N Y
pull-coord2-vec = 0 0 1
pull-coord2-start = yes
;pull-coord2-origin = 0 0 0
pull-coord3-type = constant-force
;pull-coord3-rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord3-k = 1500
pull-coord3-geometry = direction
pull-coord3-groups = 0 4
pull-coord3-dim = N N Y
pull-coord3-vec = 0 0 1
pull-coord3-start = yes
;pull-coord3-origin = 0 0 0
pull-coord4-type = constant-force
;pull-coord4-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord4-k = -1500
pull-coord4-geometry = direction
pull-coord4-groups = 0 3
pull-coord4-dim = N N Y
pull-coord4-vec = 0 0 1
pull-coord4-start = yes
;pull-coord4-origin = 0 0 0
pull-coord5-type = constant-force
;pull-coord5-rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord5-k = 1500
pull-coord5-geometry = direction
pull-coord5-groups = 0 6
pull-coord5-dim = N N Y
pull-coord5-vec = 0 0 1
pull-coord5-start = yes
;pull-coord5-origin = 0 0 0
pull-coord6-type = constant-force
;pull-coord6-rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull-coord6-k = -1500
pull-coord6-geometry = direction
pull-coord6-groups = 0 5
pull-coord6-dim = N N Y
pull-coord6-vec = 0 0 1
pull-coord6-start = yes
;pull-coord6-origin = 0 0 0
; Enforced rotation: No or Yes
rotation = Yes
; Output frequency for angle, torque and rotation potential energy for the whole group
rot-nstrout = 1
; Output frequency for per-slab data (angles, torques and slab centers)
rot-nstsout = 10
; Number of rotation groups
rot-ngroups = 2
; Rotation group name
rot-group0 = 1_NME
rot-group1 = 1_ACE
; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t
rot-type0 = flex2-t
rot-type1 = flex2-t
; Use mass-weighting of the rotation group positions
rot-massw0 = yes
rot-massw1 = yes
; Rotation vector, will get normalized
rot-vec0 = 0 0 1
rot-vec1 = 0 0 1
; Pivot point for the potentials iso, pm, rm, and rm2 [nm]
;rot-pivot0 = 2.31852e+00 2.73201e+00 10.89800e+00
; Rotation rate [degree/ps] and force constant [kJ/(mol*nm^2)]
rot-rate0 = 0.0
rot-k0 = 2000.0
rot-rate1 = 0.0
rot-k1 = 2000.0
; Slab distance for flexible axis rotation [nm]
rot-slab-dist0 = 1.5
rot-slab-dist1 = 1.5
; Minimum value of Gaussian function for the force to be evaluated (for flex* potentials)
rot-min-gauss0 = 0.001
rot-min-gauss1 = 0.001
; Value of additive constant epsilon' [nm^2] for rm2* and flex2* potentials
rot-eps0 = 0.0001
rot-eps1 = 0.0001
; Fitting method to determine angle of rotation group (rmsd, norm, or potential)
rot-fit-method0 = norm
rot-fit-method1 = norm
; For fit type 'potential', nr. of angles around the reference for which the pot. is evaluated
rot-potfit-nsteps0 = 21
rot-potfit-nsteps1 = 21
; For fit type 'potential', distance in degrees between two consecutive angles
rot-potfit-step0 = 0.25
rot-potfit-step1 = 0.25