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minimise.mdp
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minimise.mdp
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; VARIOUS PREPROCESSING OPTIONS
title = EM for shrinking
cpp = /lib/cpp
include =
;define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 10000
; 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 =
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 0
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 250
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 250
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file
nstxtcout = 100
xtc-precision = 100
; 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 = 0.8
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = reaction-field
rcoulomb-switch = 0
rcoulomb = 0.8
; 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 = 0.8
; 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 = system
; Time constant (ps) and reference temperature (K)
;tau-t = 0.1
;ref-t = 310
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semi-isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility = 4.5e-5 4.5e-5
ref-p = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed = 355616
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen-temp = 310
gen-seed = -1
; OPTIONS FOR BONDS
constraints = none ; was all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs ;Shake doesn't work for version 4.X
; 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 = 4
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 90
; Convert harmonic bonds to morse potentials
morse = no