clean

;

;	File 'mdout.mdp' was generated

;	By user: carlo (501)

;	On host: Carlos-MacBook-Pro.local

;	At date: Thu May 29 00:44:02 2014

;

; 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                   = 1000

; 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                = Linear

; number of steps for center of mass motion removal

nstcomm                  = 10

; 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                  = 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 (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                  = 10000

nstvout                  = 10000

nstfout                  = 0

; Output frequency for energies to log file and energy file

nstlog                   = 10000

nstcalcenergy            = -1

nstenergy                = 1000

; Output frequency and precision for .xtc file

nstxtcout                = 10

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                 = protein

; Selection of energy groups

energygrps               = 

; NEIGHBORSEARCHING PARAMETERS

; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)

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 drift due to the Verlet buffer in kJ/mol/ps per atom,

; a value of -1 means: use rlist

verlet-buffer-drift      = 0.0001

; nblist cut-off        

rlist                    = 0.9

; long-range cut-off for switched potentials

rlistlong                = -1

nstcalclr                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype              = pme

coulomb-modifier         = Potential-shift-Verlet

rcoulomb-switch          = 0

rcoulomb                 = 0.9

; Relative dielectric constant for the medium and the reaction field

epsilon_r                = 1

epsilon_rf               = 1

; Method for doing Van der Waals

vdw-type                 = cut-off

vdw-modifier             = Potential-shift-Verlet

; cut-off lengths       

rvdw-switch              = 0

rvdw                     = 0.9

; 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             = yes

; IMPLICIT SOLVENT ALGORITHM

implicit_solvent         = 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                 = 1

; Dielectric coefficient of the implicit solvent

gb_epsilon_solvent       = 80

; 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       = 2.092

; 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                    = 1

ref_t                    = 278

; pressure coupling     

Pcoupl                   = No

Pcoupltype               = isotropic

nstpcouple               = -1

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p                    = 0.5

compressibility          = 4.5e-5

ref_p                    = 1.0

; 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                  = yes

gen_temp                 = 278.0

gen_seed                 = -1

; OPTIONS FOR BONDS    

constraints              = all-bonds

; 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               = 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

; 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              = 0

init-lambda-state        = -1

delta-lambda             = 0

nstdhdl                  = 10

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                 = 0

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

;

;	File 'mdout.mdp' was generated

;	By user: carlo (501)

;	On host: Carlos-MacBook-Pro.local

;	At date: Thu May 29 23:17:46 2014

;

; 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                   = 1000

; 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                = Linear

; number of steps for center of mass motion removal

nstcomm                  = 10

; 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                  = 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 (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                  = 10000

nstvout                  = 10000

nstfout                  = 0

; Output frequency for energies to log file and energy file

nstlog                   = 10000

nstcalcenergy            = -1

nstenergy                = 1000

; Output frequency and precision for .xtc file

nstxtcout                = 10

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                 = protein

; Selection of energy groups

energygrps               = 

; NEIGHBORSEARCHING PARAMETERS

; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)

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 drift due to the Verlet buffer in kJ/mol/ps per atom,

; a value of -1 means: use rlist

verlet-buffer-drift      = 0.0001

; nblist cut-off        

rlist                    = 0.9

; long-range cut-off for switched potentials

rlistlong                = -1

nstcalclr                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype              = pme

coulomb-modifier         = Potential-shift-Verlet

rcoulomb-switch          = 0

rcoulomb                 = 0.9

; Relative dielectric constant for the medium and the reaction field

epsilon_r                = 1

epsilon_rf               = 1

; Method for doing Van der Waals

vdw-type                 = cut-off

vdw-modifier             = Potential-shift-Verlet

; cut-off lengths       

rvdw-switch              = 0

rvdw                     = 0.9

; 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             = yes

; IMPLICIT SOLVENT ALGORITHM

implicit_solvent         = 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                 = 1

; Dielectric coefficient of the implicit solvent

gb_epsilon_solvent       = 80

; 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       = 2.092

; 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                    = 1

ref_t                    = 278

; pressure coupling     

Pcoupl                   = No

Pcoupltype               = isotropic

nstpcouple               = -1

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau_p                    = 0.5

compressibility          = 4.5e-5

ref_p                    = 1.0

; 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                  = yes

gen_temp                 = 278.0

gen_seed                 = -1

; OPTIONS FOR BONDS    

constraints              = all-bonds

; 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               = 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

; 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              = 0

init-lambda-state        = -1

delta-lambda             = 0

nstdhdl                  = 10

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                 = 0

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