mdout.mdp

;
;	File 'mdout.mdp' was generated
;	By user: jbirgmei (259419)
;	On host: sherlock-ln02.stanford.edu
;	At date: Sun Oct 18 11:56:58 2015
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include                  = 
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define                   = 

; RUN CONTROL PARAMETERS
integrator               = sd
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000
; For exact run continuation or redoing part of a run
init-step                = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part          = 1
; mode for center of mass motion removal
comm_mode                = Angular
; number of steps for center of mass motion removal
nstcomm                  = 1000
; group(s) for center of mass motion removal
comm-grps                = 

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld-seed                  = -1

; 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 (ps^2) for minimization of flexible constraints
fcstep                   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10

; TEST PARTICLE INSERTION OPTIONS
rtpi                     = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000
; Output frequency for energies to log file and energy file
nstlog                   = 5000
nstcalcenergy            = 5000
nstenergy                = 5000
; Output frequency and precision for .xtc file
nstxtcout                = 5000
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               = 

; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
cutoff-scheme            = Group
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = no
periodic-molecules       = no
; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-drift      = 0.005
; nblist cut-off        
rlist                    = 0
; long-range cut-off for switched potentials
rlistlong                = -1
nstcalclr                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
coulomb-modifier         = Potential-shift-Verlet
rcoulomb-switch          = 0
rcoulomb                 = 0
; 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-shift-Verlet
; cut-off lengths       
rvdw-switch              = 0
rvdw                     = 0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; 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           = 0.12
; 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

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = GBSA

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = OBC
; 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                 = 0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 78.3
; Salt concentration in M for Generalized Born models
gb-saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb-obc-alpha             = 1
gb-obc-beta              = 0.8
gb-obc-gamma             = 4.85
gb-dielectric-offset     = 0.009
sa_algorithm             = ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension       = 2.25936

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl                   = no
nsttcouple               = -1
nh-chain-length          = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps                  = system
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.02
ref_t                    = 300
; pressure coupling     
pcoupl                   = No
pcoupltype               = Isotropic
nstpcouple               = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 1
compressibility          = 
ref-p                    = 
; Scaling of reference coordinates, No, All or COM
refcoord-scaling         = No

; OPTIONS FOR QMMM calculations
QMMM                     = no
; Groups treated Quantum Mechanically
QMMM-grps                = 
; QM method             
QMmethod                 = 
; QMMM scheme           
QMMMscheme               = normal
; QM basisset           
QMbasis                  = 
; QM charge             
QMcharge                 = 
; QM multiplicity       
QMmult                   = 
; Surface Hopping       
SH                       = 
; CAS space options     
CASorbitals              = 
CASelectrons             = 
SAon                     = 
SAoff                    = 
SAsteps                  = 
; Scale factor for MM charges
MMChargeScaleFactor      = 1
; Optimization of QM subsystem
bOPT                     = 
bTS                      = 

; SIMULATED ANNEALING  
; Type of annealing for each temperature group (no/single/periodic)
annealing                = 
; Number of time points to use for specifying annealing in each group
annealing-npoints        = 
; List of times at the annealing points for each group
annealing-time           = 
; Temp. at each annealing point, for each group.
annealing-temp           = 

; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = no
gen-temp                 = 300
gen_seed                 = -1

; OPTIONS FOR BONDS    
constraints              = hbonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 0.0001
; 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           = 

; WALLS                
; Number of walls, type, atom types, densities and box-z scale factor for Ewald
nwall                    = 0
wall-type                = 9-3
wall-r-linpot            = -1
wall-atomtype            = 
wall-density             = 
wall-ewald-zfac          = 3

; COM PULLING          
; Pull type: no, umbrella, constraint or constant-force
pull                     = no

; ENFORCED ROTATION    
; Enforced rotation: No or Yes
rotation                 = no

; 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) and S to energy file
nstorireout              = 100

; Free energy variables
free-energy              = no
couple-moltype           = 
couple-lambda0           = vdw-q
couple-lambda1           = vdw-q
couple-intramol          = no
init-lambda              = -1
init-lambda-state        = -1
delta-lambda             = 0
nstdhdl                  = 50
fep-lambdas              = 
mass-lambdas             = 
coul-lambdas             = 
vdw-lambdas              = 
bonded-lambdas           = 
restraint-lambdas        = 
temperature-lambdas      = 
calc-lambda-neighbors    = 1
init-lambda-weights      = 
dhdl-print-energy        = no
sc-alpha                 = 0
sc-power                 = 1
sc-r-power               = 6
sc-sigma                 = 0.3
sc-coul                  = no
separate-dhdl-file       = yes
dhdl-derivatives         = yes
dh_hist_size             = 0
dh_hist_spacing          = 0.1

; Non-equilibrium MD stuff
acc-grps                 = 
accelerate               = 
freezegrps               = 
freezedim                = 
cos-acceleration         = 0
deform                   = 

; simulated tempering variables
simulated-tempering      = no
simulated-tempering-scaling = geometric
sim-temp-low             = 300
sim-temp-high            = 300

; 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                     = 

; AdResS parameters    
adress                   = no

; User defined thingies
user1-grps               = 
user2-grps               = 
userint1                 = 0
userint2                 = 0
userint3                 = 0
userint4                 = 0
userreal1                = 0
userreal2                = 0
userreal3                = 0
userreal4                = 0