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; VARIOUS PREPROCESSING OPTIONS | ||
; Preprocessor - specify a full path if necessary. | ||
include = | ||
define = | ||
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; RUN CONTROL PARAMETERS | ||
integrator = sd | ||
; Start time and timestep in ps | ||
tinit = 0 | ||
dt = 0.020 | ||
nsteps = 1000000 | ||
; 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 = 10 | ||
; group(s) for center of mass motion removal | ||
comm_grps = | ||
;system | ||
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; LANGEVIN DYNAMICS OPTIONS | ||
; Friction coefficient (amu/ps) and random seed | ||
ld-seed = -1 | ||
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; OUTPUT CONTROL OPTIONS | ||
; Output frequency for coords (x), velocities (v) and forces (f) | ||
nstxout = 0 | ||
nstvout = 0 | ||
nstfout = 0 | ||
; Output frequency for energies to log file and energy file | ||
nstlog = 100 | ||
nstenergy = 100 | ||
; Output frequency and precision for xtc file | ||
nstxout-compressed = 100 | ||
compressed-x-precision = 1000 | ||
; This selects the subset of atoms for the xtc file. You can | ||
; select multiple groups. By default all atoms will be written. | ||
compressed-x-grps = System ;Protein | ||
; Selection of energy groups | ||
energygrps = VNL EST C1 NO | ||
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; NEIGHBORSEARCHING PARAMETERS | ||
; nblist update frequency | ||
nstlist = 10 | ||
; 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 = 1.5 | ||
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; OPTIONS FOR ELECTROSTATICS AND VDW | ||
; Method for doing electrostatics | ||
coulombtype = Cut-off | ||
rcoulomb-switch = 0 | ||
rcoulomb = 1.5 | ||
; Relative dielectric constant for the medium and the reaction field | ||
epsilon_r = 1 | ||
epsilon_rf = 1 | ||
; Method for doing Van der Waals | ||
vdwtype = user | ||
; cut-off lengths | ||
rvdw-switch = 0 | ||
rvdw = 1.5 | ||
; Apply long range dispersion corrections for Energy and Pressure | ||
DispCorr = EnerPres | ||
; Extension of the potential lookup tables beyond the cut-off | ||
table-extension = 1.0 | ||
; Seperate tables between energy group pairs | ||
energygrp_table = VNL VNL VNL EST VNL C1 VNL NO EST EST EST C1 EST NO C1 C1 C1 NO NO NO | ||
; Spacing for the PME/PPPM FFT grid | ||
fourierspacing = 0.12 | ||
; FFT grid size, when a value is 0 fourierspacing will be used | ||
fourier_nx = 0 | ||
fourier_ny = 0 | ||
fourier_nz = 0 | ||
; EWALD/PME/PPPM parameters | ||
pme_order = 4 | ||
ewald_rtol = 1e-05 | ||
ewald_geometry = 3d | ||
epsilon_surface = 0 | ||
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; OPTIONS FOR WEAK COUPLING ALGORITHMS | ||
; Temperature coupling | ||
tcoupl = berendsen | ||
; Groups to couple separately | ||
tc-grps = System | ||
; Time constant (ps) and reference temperature (K) | ||
tau_t = 1.0 | ||
ref_t = 300 | ||
; Pressure coupling | ||
Pcoupl = berendsen | ||
pcoupltype = isotropic | ||
; Time constant (ps), compressibility (1/bar) and reference P (bar) | ||
tau_p = 2.0 | ||
compressibility = 4.5e-5 | ||
ref_p = 1.0 | ||
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; GENERATE VELOCITIES FOR STARTUP RUN | ||
gen_vel = yes | ||
gen_temp = 300 | ||
gen_seed = -1 | ||
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; OPTIONS FOR BONDS | ||
constraints = none | ||
; Type of constraint algorithm | ||
constraint_algorithm = LINCS | ||
; 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 = 2 | ||
; 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 | ||
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; ENERGY GROUP EXCLUSIONS | ||
; Pairs of energy groups for which all non-bonded interactions are excluded | ||
energygrp_excl = | ||
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cutoff-scheme = Group |
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