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7_prod.mdp
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7_prod.mdp
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;MDP-file production run: 10 000 ns.
; this protocol now generates velocities this is useful for generating parallel runs with different random seeds
; random seeds are selected randomly by grompp here
; VARIOUS PREPROCESSING OPTIONS
include =
define = -DCUSTOMPOSRES ; NO RESTRAINTS DEFINED HERE
; will trigger the inclusion of posre.itp into your topology, used for implementing position restraints.
; here we assume that in posres.itp file all force constants have been changed to POSRES_FC
; see this link for details http://mdsquad.wikia.com/wiki/Change_position_restraint_force_constant_in_MDP
;1000 kJ mol-1 nm-2 is the default constant
;to match AMBER we need 100 kcal/mol/A2, which is 418 kJ/mol/A2 - we set 500
; RUN CONTROL PARAMETERS
integrator = md ; Steepest descent integrator
nsteps = 5000000000 ; 5 000 000 000 = 10 microsecond
init-step = 0 ; For exact run continuation or redoing part of a run
simulation-part = 1 ; Part index is updated automatically on checkpointing (keeps files separate)
comm-mode = Linear ; mode for center of mass motion removal
nstcomm = 100 ; number of steps for center of mass motion removal
comm-grps = System ; group(s) for center of mass motion removal default is the whole system;
dt = 0.002 ; this is only for MD
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 100.0
emstep = 0.01
; 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 = 1000
nstcalcenergy = 100 ; why less -> looks like this is needed for thermostats/barostats
nstenergy = 1000
; Output frequency and precision for .xtc file
nstxout-compressed = 500000 ; every 1 ns
compressed-x-precision = 1000
; 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 =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns-type = Grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 1.4 ; actually will be ignore and calculated from verlet-buffer-tolerance
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = None ; change from default Potential-shift-Verlet because Amber does not use shift.
rcoulomb-switch = 0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon-rf = 0
; Method for doing Van der Waals
vdwtype = Cut-off
vdw-modifier = Potential-switch ; this is for CHARMM
; cut-off lengths
rvdw_switch = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No ; Looks like CHARMM does not use it
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.1 ; for CHARMM
; 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 ; left the same as in amber setup - think this is only for Ewald
ewald-geometry = 3d
epsilon-surface = 0
; OPTIONS FOR BONDS
constraints = h-bonds ; the same as used in CHARMM
; Type of constraint algorithm
constraint_algorithm = LINCS ; this is better than SHAKE so we retain it
; Do not constrain the start configuration
continuation = no
; 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 = 8 ; in MD we will set this to 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Below is only relevant for MD
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = yes
gen-temp = 300
gen-seed = -1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1 ; the frequency of coupling the temperarure, -1 is automatic = nstlist for md integrator
; Groups to couple separately
tc-grps = System ; NOTE: Group name "System" is defined if you are NOT using an index file. But better to generate a default index file anyway.
; Time constant (ps) and reference temperature (K)
tau-t = 1 ; 1 ps as used in Amber paper, but we might need to research and use different for large scale dynamics!
ref-t = 300
; pressure coupling
pcoupl = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility = 4.5e-5 ; for water
ref-p = 1 ; 1 bar
; Scaling of reference coordinates, No, All or COM
refcoord-scaling = com ; The reference coordinates are scaled with the scaling matrix of the pressure coupling.
; ??? check if com is better?
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp-excl =