234 lines
7.6 KiB
Plaintext
234 lines
7.6 KiB
Plaintext
|
;
|
||
|
|
; File 'mdout.mdp' was generated
|
||
|
|
; By user: bert (1001)
|
||
|
|
; On host: bertp3
|
||
|
|
; At date: Sat Dec 4 13:41:42 2004
|
||
|
|
;
|
||
|
|
|
||
|
|
; VARIOUS PREPROCESSING OPTIONS
|
||
|
|
include =
|
||
|
|
define =
|
||
|
|
|
||
|
|
; RUN CONTROL PARAMETERS
|
||
|
|
integrator = md
|
||
|
|
; Start time and timestep in ps
|
||
|
|
tinit = 0
|
||
|
|
dt = 0.002
|
||
|
|
nsteps = 500000
|
||
|
|
; For exact run continuation or redoing part of a run
|
||
|
|
init_step = 0
|
||
|
|
; mode for center of mass motion removal
|
||
|
|
comm-mode = Angular
|
||
|
|
; number of steps for center of mass motion removal
|
||
|
|
nstcomm = 1
|
||
|
|
; group(s) for center of mass motion removal
|
||
|
|
comm-grps =
|
||
|
|
|
||
|
|
; LANGEVIN DYNAMICS OPTIONS
|
||
|
|
; Temperature, friction coefficient (amu/ps) and random seed
|
||
|
|
bd-fric = 0
|
||
|
|
ld-seed = 1993
|
||
|
|
|
||
|
|
; ENERGY MINIMIZATION OPTIONS
|
||
|
|
; Force tolerance and initial step-size
|
||
|
|
emtol = 10
|
||
|
|
emstep = 0.01
|
||
|
|
; Max number of iterations in relax_shells
|
||
|
|
niter = 20
|
||
|
|
; Step size (1/ps^2) for minimization of flexible constraints
|
||
|
|
fcstep = 0
|
||
|
|
; Frequency of steepest descents steps when doing CG
|
||
|
|
nstcgsteep = 1000
|
||
|
|
nbfgscorr = 10
|
||
|
|
|
||
|
|
; OUTPUT CONTROL OPTIONS
|
||
|
|
; Output frequency for coords (x), velocities (v) and forces (f)
|
||
|
|
nstxout = 5000
|
||
|
|
nstvout = 5000
|
||
|
|
nstfout = 0
|
||
|
|
; Checkpointing helps you continue after crashes
|
||
|
|
nstcheckpoint = 1000
|
||
|
|
; Output frequency for energies to log file and energy file
|
||
|
|
nstlog = 500
|
||
|
|
nstenergy = 500
|
||
|
|
; Output frequency and precision for xtc file
|
||
|
|
nstxtcout = 500
|
||
|
|
xtc-precision = 1000
|
||
|
|
; This selects the subset of atoms for the xtc file. You can
|
||
|
|
; select multiple groups. By default all atoms will be written.
|
||
|
|
xtc-grps =
|
||
|
|
; Selection of energy groups
|
||
|
|
energygrps = System
|
||
|
|
|
||
|
|
; long-range cut-off for switched potentials
|
||
|
|
rlistlong = -1
|
||
|
|
cutoff-scheme = Verlet
|
||
|
|
|
||
|
|
; NEIGHBORSEARCHING PARAMETERS
|
||
|
|
; nblist update frequency
|
||
|
|
nstlist = 50
|
||
|
|
; 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 = 0.85
|
||
|
|
|
||
|
|
|
||
|
|
; OPTIONS FOR ELECTROSTATICS AND VDW
|
||
|
|
; Method for doing electrostatics
|
||
|
|
coulombtype = Cut-off
|
||
|
|
rcoulomb-switch = 0
|
||
|
|
rcoulomb = 0.85
|
||
|
|
; Dielectric constant (DC) for cut-off or DC of reaction field
|
||
|
|
epsilon-r = 1
|
||
|
|
; Method for doing Van der Waals
|
||
|
|
vdw-type = Cut-off
|
||
|
|
; cut-off lengths
|
||
|
|
rvdw-switch = 0
|
||
|
|
rvdw = 0.85
|
||
|
|
; Apply long range dispersion corrections for Energy and Pressure
|
||
|
|
DispCorr = Enerpres
|
||
|
|
; Extension of the potential lookup tables beyond the cut-off
|
||
|
|
table-extension = 1
|
||
|
|
; 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
|
||
|
|
optimize_fft = no
|
||
|
|
|
||
|
|
; GENERALIZED BORN ELECTROSTATICS
|
||
|
|
; Algorithm for calculating Born radii
|
||
|
|
gb_algorithm = Still
|
||
|
|
; Frequency of calculating the Born radii inside rlist
|
||
|
|
nstgbradii = 1
|
||
|
|
; Cutoff for Born radii calculation; the contribution from atoms
|
||
|
|
; between rlist and rgbradii is updated every nstlist steps
|
||
|
|
rgbradii = 2
|
||
|
|
; Salt concentration in M for Generalized Born models
|
||
|
|
gb_saltconc = 0
|
||
|
|
|
||
|
|
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
|
||
|
|
implicit_solvent = No
|
||
|
|
|
||
|
|
; OPTIONS FOR WEAK COUPLING ALGORITHMS
|
||
|
|
; Temperature coupling
|
||
|
|
Tcoupl = v-rescale
|
||
|
|
; Groups to couple separately
|
||
|
|
tc-grps = System
|
||
|
|
; Time constant (ps) and reference temperature (K)
|
||
|
|
tau_t = 0.1
|
||
|
|
ref_t = 100
|
||
|
|
; Pressure coupling
|
||
|
|
Pcoupl = no
|
||
|
|
Pcoupltype = isotropic
|
||
|
|
; Time constant (ps), compressibility (1/bar) and reference P (bar)
|
||
|
|
tau_p = 0.5
|
||
|
|
compressibility = 4.5e-5
|
||
|
|
ref_p = 1.0
|
||
|
|
|
||
|
|
; SIMULATED ANNEALING
|
||
|
|
; Type of annealing for each temperature group (no/single/periodic)
|
||
|
|
annealing = single
|
||
|
|
; Number of time points to use for specifying annealing in each group
|
||
|
|
annealing_npoints = 2
|
||
|
|
; List of times at the annealing points for each group
|
||
|
|
annealing_time = 0 1000
|
||
|
|
; Temp. at each annealing point, for each group.
|
||
|
|
annealing_temp = 100 25
|
||
|
|
|
||
|
|
; GENERATE VELOCITIES FOR STARTUP RUN
|
||
|
|
gen_vel = yes
|
||
|
|
gen_temp = 100.0
|
||
|
|
gen_seed = 173529
|
||
|
|
|
||
|
|
; OPTIONS FOR BONDS
|
||
|
|
constraints = all-bonds
|
||
|
|
; Type of constraint algorithm
|
||
|
|
constraint-algorithm = Lincs
|
||
|
|
; Do not constrain the start configuration
|
||
|
|
unconstrained-start = no
|
||
|
|
; 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
|
||
|
|
|
||
|
|
; ENERGY GROUP EXCLUSIONS
|
||
|
|
; Pairs of energy groups for which all non-bonded interactions are excluded
|
||
|
|
energygrp_excl =
|
||
|
|
|
||
|
|
; NMR refinement stuff
|
||
|
|
; Distance restraints type: No, Simple or Ensemble
|
||
|
|
disre = No
|
||
|
|
; Force weighting of pairs in one distance restraint: Conservative or Equal
|
||
|
|
disre-weighting = Conservative
|
||
|
|
; Use sqrt of the time averaged times the instantaneous violation
|
||
|
|
disre-mixed = no
|
||
|
|
disre-fc = 1000
|
||
|
|
disre-tau = 0
|
||
|
|
; Output frequency for pair distances to energy file
|
||
|
|
nstdisreout = 100
|
||
|
|
; Orientation restraints: No or Yes
|
||
|
|
orire = no
|
||
|
|
; Orientation restraints force constant and tau for time averaging
|
||
|
|
orire-fc = 0
|
||
|
|
orire-tau = 0
|
||
|
|
orire-fitgrp =
|
||
|
|
; Output frequency for trace(SD) to energy file
|
||
|
|
nstorireout = 100
|
||
|
|
|
||
|
|
; Free energy control stuff
|
||
|
|
free-energy = no
|
||
|
|
init-lambda = 0
|
||
|
|
delta-lambda = 0
|
||
|
|
sc-alpha = 0
|
||
|
|
sc-sigma = 0.3
|
||
|
|
|
||
|
|
; Non-equilibrium MD stuff
|
||
|
|
acc-grps =
|
||
|
|
accelerate =
|
||
|
|
freezegrps =
|
||
|
|
freezedim =
|
||
|
|
cos-acceleration = 0
|
||
|
|
|
||
|
|
; Electric fields
|
||
|
|
; Format is number of terms (int) and for all terms an amplitude (real)
|
||
|
|
; and a phase angle (real)
|
||
|
|
E-x =
|
||
|
|
E-xt =
|
||
|
|
E-y =
|
||
|
|
E-yt =
|
||
|
|
E-z =
|
||
|
|
E-zt =
|
||
|
|
|
||
|
|
; User defined thingies
|
||
|
|
user1-grps =
|
||
|
|
user2-grps =
|
||
|
|
userint1 = 0
|
||
|
|
userint2 = 0
|
||
|
|
userint3 = 0
|
||
|
|
userint4 = 0
|
||
|
|
userreal1 = 0
|
||
|
|
userreal2 = 0
|
||
|
|
userreal3 = 0
|
||
|
|
userreal4 = 0
|