gromacs.input

Implementation level

Type

Status

CML extraction template

image1

HTML5 representation

image2

Template attributes

Attribute

Value

source

GROMACS input

id

gromacs.input

name

GROMACS input

xml:base

topTemplate.xml

Input

;
;   File 'mdout.mdp' was generated
;   By user: unknown (1095)
;   On host: node2178
;   At date: Tue Dec 11 15:42:14 2018
;

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

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.0005
nsteps                   = 80000000
; 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                  = 1000
nstvout                  = 1000
nstfout                  = 1000
; Output frequency for energies to log file and energy file
nstlog                   = 500
nstcalcenergy            = -1
nstenergy                = 1000
; Output frequency and precision for .xtc file
nstxout-compressed       = 2000
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        = SOL LIN LI
; Selection of energy groups
energygrps               = SOL LIN LI

; 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                    = 1.7
; 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                 = 1.7
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdwtype                  = cut-off
vdw-modifier             = Potential-shift-Verlet
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 1.7
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; 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-rtol-lj            = 0.001
lj-pme-comb-rule         = Geometric
ewald_geometry           = 3d
epsilon_surface          = 0

; 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       = -1

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl                   = Berendsen
nsttcouple               = 2
nh-chain-length          = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps                  = SOL LIN LI
; Time constant (ps) and reference temperature (K)
tau-t                    = 0.1 0.02 0.1
ref-t                    = 300 300 300
; pressure coupling
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
nstpcouple               = 2
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 1.0
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                  = no
gen-temp                 = 300
gen-seed                 = 173529

; OPTIONS FOR BONDS
constraints              = all-bonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
continuation             = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = yes
; 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

; Group to display and/or manipulate in interactive MD session
IMD-group                =

; 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                     =

; Ion/water position swapping for computational electrophysiology setups
; Swap positions along direction: no, X, Y, Z
swapcoords               = no

; 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

Output text

  1<comment class="example.output" id="gromacs.input">
  2        <module id="gromacs.input">
  3            <scalar dataType="xsd:string" dictRef="gm:include">-I../top</scalar>
  4            <scalar dataType="xsd:string" dictRef="gm:define" />
  5            <scalar dataType="xsd:string" dictRef="gm:integrator">md</scalar>
  6            <scalar dataType="xsd:string" dictRef="gm:tinit">0</scalar>
  7            <scalar dataType="xsd:string" dictRef="gm:dt">0.0005</scalar>
  8            <scalar dataType="xsd:string" dictRef="gm:nsteps">8000000</scalar>
  9            <scalar dataType="xsd:string" dictRef="gm:init.step">0</scalar>
 10            <scalar dataType="xsd:string" dictRef="gm:simulation.part">1</scalar>
 11            <scalar dataType="xsd:string" dictRef="gm:comm.mode">Linear</scalar>
 12            <scalar dataType="xsd:string" dictRef="gm:nstcomm">10</scalar>
 13            <scalar dataType="xsd:string" dictRef="gm:comm.grps" />
 14            <scalar dataType="xsd:string" dictRef="gm:bd.fric">0</scalar>
 15            <scalar dataType="xsd:string" dictRef="gm:ld.seed">1993</scalar>
 16            <scalar dataType="xsd:string" dictRef="gm:emtol">10</scalar>
 17            <scalar dataType="xsd:string" dictRef="gm:emstep">0.01</scalar>
 18            <scalar dataType="xsd:string" dictRef="gm:niter">20</scalar>
 19            <scalar dataType="xsd:string" dictRef="gm:fcstep">0</scalar>
 20            <scalar dataType="xsd:string" dictRef="gm:nstcgsteep">1000</scalar>
 21            <scalar dataType="xsd:string" dictRef="gm:nbfgscorr">10</scalar>
 22            <scalar dataType="xsd:string" dictRef="gm:rtpi">0.05</scalar>
 23            <scalar dataType="xsd:string" dictRef="gm:nstxout">1000</scalar>
 24            <scalar dataType="xsd:string" dictRef="gm:nstvout">1000</scalar>
 25            <scalar dataType="xsd:string" dictRef="gm:nstfout">1000</scalar>
 26            <scalar dataType="xsd:string" dictRef="gm:nstlog">500</scalar>
 27            <scalar dataType="xsd:string" dictRef="gm:nstcalcenergy">-1</scalar>
 28            <scalar dataType="xsd:string" dictRef="gm:nstenergy">1000</scalar>
 29            <scalar dataType="xsd:string" dictRef="gm:nstxout.compressed">2000</scalar>
 30            <scalar dataType="xsd:string" dictRef="gm:compressed.x.precision">1000</scalar>
 31            <scalar dataType="xsd:string" dictRef="gm:compressed.x.grps">LIG COT TBA</scalar>
 32            <scalar dataType="xsd:string" dictRef="gm:energygrps">LIG COT TBA</scalar>
 33            <scalar dataType="xsd:string" dictRef="gm:cutoff.scheme">Verlet</scalar>
 34            <scalar dataType="xsd:string" dictRef="gm:nstlist">10</scalar>
 35            <scalar dataType="xsd:string" dictRef="gm:ns.type">grid</scalar>
 36            <scalar dataType="xsd:string" dictRef="gm:pbc">xyz</scalar>
 37            <scalar dataType="xsd:string" dictRef="gm:periodic.molecules">no</scalar>
 38            <scalar dataType="xsd:string" dictRef="gm:verlet.buffer.tolerance">0.005</scalar>
 39            <scalar dataType="xsd:string" dictRef="gm:rlist">1.7</scalar>
 40            <scalar dataType="xsd:string" dictRef="gm:rlistlong">-1</scalar>
 41            <scalar dataType="xsd:string" dictRef="gm:nstcalclr">-1</scalar>
 42            <scalar dataType="xsd:string" dictRef="gm:coulombtype">PME</scalar>
 43            <scalar dataType="xsd:string" dictRef="gm:coulomb.modifier">Potential-shift-Verlet</scalar>
 44            <scalar dataType="xsd:string" dictRef="gm:rcoulomb.switch">0</scalar>
 45            <scalar dataType="xsd:string" dictRef="gm:rcoulomb">1.7</scalar>
 46            <scalar dataType="xsd:string" dictRef="gm:epsilon.r">1</scalar>
 47            <scalar dataType="xsd:string" dictRef="gm:epsilon.rf">1</scalar>
 48            <scalar dataType="xsd:string" dictRef="gm:vdwtype">cut-off</scalar>
 49            <scalar dataType="xsd:string" dictRef="gm:vdw.modifier">Potential-shift-Verlet</scalar>
 50            <scalar dataType="xsd:string" dictRef="gm:rvdw.switch">0</scalar>
 51            <scalar dataType="xsd:string" dictRef="gm:rvdw">1.7</scalar>
 52            <scalar dataType="xsd:string" dictRef="gm:dispcorr">EnerPres</scalar>
 53            <scalar dataType="xsd:string" dictRef="gm:table.extension">1</scalar>
 54            <scalar dataType="xsd:string" dictRef="gm:energygrp.table" />
 55            <scalar dataType="xsd:string" dictRef="gm:fourierspacing">0.12</scalar>
 56            <scalar dataType="xsd:string" dictRef="gm:fourier.nx">0</scalar>
 57            <scalar dataType="xsd:string" dictRef="gm:fourier.ny">0</scalar>
 58            <scalar dataType="xsd:string" dictRef="gm:fourier.nz">0</scalar>
 59            <scalar dataType="xsd:string" dictRef="gm:pme.order">4</scalar>
 60            <scalar dataType="xsd:string" dictRef="gm:ewald.rtol">1e-05</scalar>
 61            <scalar dataType="xsd:string" dictRef="gm:ewald.rtol.lj">0.001</scalar>
 62            <scalar dataType="xsd:string" dictRef="gm:lj.pme.comb.rule">Geometric</scalar>
 63            <scalar dataType="xsd:string" dictRef="gm:ewald.geometry">3d</scalar>
 64            <scalar dataType="xsd:string" dictRef="gm:epsilon.surface">0</scalar>
 65            <scalar dataType="xsd:string" dictRef="gm:implicit.solvent">No</scalar>
 66            <scalar dataType="xsd:string" dictRef="gm:gb.algorithm">Still</scalar>
 67            <scalar dataType="xsd:string" dictRef="gm:nstgbradii">1</scalar>
 68            <scalar dataType="xsd:string" dictRef="gm:rgbradii">1</scalar>
 69            <scalar dataType="xsd:string" dictRef="gm:gb.epsilon.solvent">80</scalar>
 70            <scalar dataType="xsd:string" dictRef="gm:gb.saltconc">0</scalar>
 71            <scalar dataType="xsd:string" dictRef="gm:gb.obc.alpha">1</scalar>
 72            <scalar dataType="xsd:string" dictRef="gm:gb.obc.beta">0.8</scalar>
 73            <scalar dataType="xsd:string" dictRef="gm:gb.obc.gamma">4.85</scalar>
 74            <scalar dataType="xsd:string" dictRef="gm:gb.dielectric.offset">0.009</scalar>
 75            <scalar dataType="xsd:string" dictRef="gm:sa.algorithm">Ace-approximation</scalar>
 76            <scalar dataType="xsd:string" dictRef="gm:sa.surface.tension">-1</scalar>
 77            <scalar dataType="xsd:string" dictRef="gm:tcoupl">Berendsen</scalar>
 78            <scalar dataType="xsd:string" dictRef="gm:nsttcouple">2</scalar>
 79            <scalar dataType="xsd:string" dictRef="gm:nh.chain.length">10</scalar>
 80            <scalar dataType="xsd:string" dictRef="gm:print.nose.hoover.chain.variables">no</scalar>
 81            <scalar dataType="xsd:string" dictRef="gm:tc.grps">COT TBA LIG</scalar>
 82            <scalar dataType="xsd:string" dictRef="gm:tau.t">0.02 0.1 0.1</scalar>
 83            <scalar dataType="xsd:string" dictRef="gm:ref.t">300 300 300</scalar>
 84            <scalar dataType="xsd:string" dictRef="gm:pcoupl">Parrinello-Rahman</scalar>
 85            <scalar dataType="xsd:string" dictRef="gm:pcoupltype">Isotropic</scalar>
 86            <scalar dataType="xsd:string" dictRef="gm:nstpcouple">2</scalar>
 87            <scalar dataType="xsd:string" dictRef="gm:tau.p">4.0</scalar>
 88            <scalar dataType="xsd:string" dictRef="gm:compressibility">4.5e-5</scalar>
 89            <scalar dataType="xsd:string" dictRef="gm:ref.p">1.0</scalar>
 90            <scalar dataType="xsd:string" dictRef="gm:refcoord.scaling">No</scalar>
 91            <scalar dataType="xsd:string" dictRef="gm:qmmm">no</scalar>
 92            <scalar dataType="xsd:string" dictRef="gm:qmmm.grps" />
 93            <scalar dataType="xsd:string" dictRef="gm:qmmethod" />
 94            <scalar dataType="xsd:string" dictRef="gm:qmmmscheme">normal</scalar>
 95            <scalar dataType="xsd:string" dictRef="gm:qmbasis" />
 96            <scalar dataType="xsd:string" dictRef="gm:qmcharge" />
 97            <scalar dataType="xsd:string" dictRef="gm:qmmult" />
 98            <scalar dataType="xsd:string" dictRef="gm:sh" />
 99            <scalar dataType="xsd:string" dictRef="gm:casorbitals" />
100            <scalar dataType="xsd:string" dictRef="gm:caselectrons" />
101            <scalar dataType="xsd:string" dictRef="gm:saon" />
102            <scalar dataType="xsd:string" dictRef="gm:saoff" />
103            <scalar dataType="xsd:string" dictRef="gm:sasteps" />
104            <scalar dataType="xsd:string" dictRef="gm:mmchargescalefactor">1</scalar>
105            <scalar dataType="xsd:string" dictRef="gm:bopt" />
106            <scalar dataType="xsd:string" dictRef="gm:bts" />
107            <scalar dataType="xsd:string" dictRef="gm:annealing" />
108            <scalar dataType="xsd:string" dictRef="gm:annealing.npoints" />
109            <scalar dataType="xsd:string" dictRef="gm:annealing.time" />
110            <scalar dataType="xsd:string" dictRef="gm:annealing.temp" />
111            <scalar dataType="xsd:string" dictRef="gm:gen.vel">no</scalar>
112            <scalar dataType="xsd:string" dictRef="gm:gen.temp">300</scalar>
113            <scalar dataType="xsd:string" dictRef="gm:gen.seed">173529</scalar>
114            <scalar dataType="xsd:string" dictRef="gm:constraints">all-bonds</scalar>
115            <scalar dataType="xsd:string" dictRef="gm:constraint.algorithm">Lincs</scalar>
116            <scalar dataType="xsd:string" dictRef="gm:continuation">yes</scalar>
117            <scalar dataType="xsd:string" dictRef="gm:shake.sor">yes</scalar>
118            <scalar dataType="xsd:string" dictRef="gm:shake.tol">0.0001</scalar>
119            <scalar dataType="xsd:string" dictRef="gm:lincs.order">4</scalar>
120            <scalar dataType="xsd:string" dictRef="gm:lincs.iter">1</scalar>
121            <scalar dataType="xsd:string" dictRef="gm:lincs.warnangle">30</scalar>
122            <scalar dataType="xsd:string" dictRef="gm:morse">no</scalar>
123            <scalar dataType="xsd:string" dictRef="gm:energygrp.excl" />
124            <scalar dataType="xsd:string" dictRef="gm:nwall">0</scalar>
125            <scalar dataType="xsd:string" dictRef="gm:wall.type">9-3</scalar>
126            <scalar dataType="xsd:string" dictRef="gm:wall.r.linpot">-1</scalar>
127            <scalar dataType="xsd:string" dictRef="gm:wall.atomtype" />
128            <scalar dataType="xsd:string" dictRef="gm:wall.density" />
129            <scalar dataType="xsd:string" dictRef="gm:wall.ewald.zfac">3</scalar>
130            <scalar dataType="xsd:string" dictRef="gm:pull">no</scalar>
131            <scalar dataType="xsd:string" dictRef="gm:rotation">no</scalar>
132            <scalar dataType="xsd:string" dictRef="gm:imd.group" />
133            <scalar dataType="xsd:string" dictRef="gm:disre">No</scalar>
134            <scalar dataType="xsd:string" dictRef="gm:disre.weighting">Conservative</scalar>
135            <scalar dataType="xsd:string" dictRef="gm:disre.mixed">no</scalar>
136            <scalar dataType="xsd:string" dictRef="gm:disre.fc">1000</scalar>
137            <scalar dataType="xsd:string" dictRef="gm:disre.tau">0</scalar>
138            <scalar dataType="xsd:string" dictRef="gm:nstdisreout">100</scalar>
139            <scalar dataType="xsd:string" dictRef="gm:orire">no</scalar>
140            <scalar dataType="xsd:string" dictRef="gm:orire.fc">0</scalar>
141            <scalar dataType="xsd:string" dictRef="gm:orire.tau">0</scalar>
142            <scalar dataType="xsd:string" dictRef="gm:orire.fitgrp" />
143            <scalar dataType="xsd:string" dictRef="gm:nstorireout">100</scalar>
144            <scalar dataType="xsd:string" dictRef="gm:free.energy">no</scalar>
145            <scalar dataType="xsd:string" dictRef="gm:couple.moltype" />
146            <scalar dataType="xsd:string" dictRef="gm:couple.lambda0">vdw-q</scalar>
147            <scalar dataType="xsd:string" dictRef="gm:couple.lambda1">vdw-q</scalar>
148            <scalar dataType="xsd:string" dictRef="gm:couple.intramol">no</scalar>
149            <scalar dataType="xsd:string" dictRef="gm:init.lambda">0</scalar>
150            <scalar dataType="xsd:string" dictRef="gm:init.lambda.state">-1</scalar>
151            <scalar dataType="xsd:string" dictRef="gm:delta.lambda">0</scalar>
152            <scalar dataType="xsd:string" dictRef="gm:nstdhdl">10</scalar>
153            <scalar dataType="xsd:string" dictRef="gm:fep.lambdas" />
154            <scalar dataType="xsd:string" dictRef="gm:mass.lambdas" />
155            <scalar dataType="xsd:string" dictRef="gm:coul.lambdas" />
156            <scalar dataType="xsd:string" dictRef="gm:vdw.lambdas" />
157            <scalar dataType="xsd:string" dictRef="gm:bonded.lambdas" />
158            <scalar dataType="xsd:string" dictRef="gm:restraint.lambdas" />
159            <scalar dataType="xsd:string" dictRef="gm:temperature.lambdas" />
160            <scalar dataType="xsd:string" dictRef="gm:calc.lambda.neighbors">1</scalar>
161            <scalar dataType="xsd:string" dictRef="gm:init.lambda.weights" />
162            <scalar dataType="xsd:string" dictRef="gm:dhdl.print.energy">no</scalar>
163            <scalar dataType="xsd:string" dictRef="gm:sc.alpha">0</scalar>
164            <scalar dataType="xsd:string" dictRef="gm:sc.power">0</scalar>
165            <scalar dataType="xsd:string" dictRef="gm:sc.r.power">6</scalar>
166            <scalar dataType="xsd:string" dictRef="gm:sc.sigma">0.3</scalar>
167            <scalar dataType="xsd:string" dictRef="gm:sc.coul">no</scalar>
168            <scalar dataType="xsd:string" dictRef="gm:separate.dhdl.file">yes</scalar>
169            <scalar dataType="xsd:string" dictRef="gm:dhdl.derivatives">yes</scalar>
170            <scalar dataType="xsd:string" dictRef="gm:dh.hist.size">0</scalar>
171            <scalar dataType="xsd:string" dictRef="gm:dh.hist.spacing">0.1</scalar>
172            <scalar dataType="xsd:string" dictRef="gm:acc.grps" />
173            <scalar dataType="xsd:string" dictRef="gm:accelerate" />
174            <scalar dataType="xsd:string" dictRef="gm:freezegrps" />
175            <scalar dataType="xsd:string" dictRef="gm:freezedim" />
176            <scalar dataType="xsd:string" dictRef="gm:cos.acceleration">0</scalar>
177            <scalar dataType="xsd:string" dictRef="gm:deform" />
178            <scalar dataType="xsd:string" dictRef="gm:simulated.tempering">no</scalar>
179            <scalar dataType="xsd:string" dictRef="gm:simulated.tempering.scaling">geometric</scalar>
180            <scalar dataType="xsd:string" dictRef="gm:sim.temp.low">300</scalar>
181            <scalar dataType="xsd:string" dictRef="gm:sim.temp.high">300</scalar>
182            <scalar dataType="xsd:string" dictRef="gm:e.x" />
183            <scalar dataType="xsd:string" dictRef="gm:e.xt" />
184            <scalar dataType="xsd:string" dictRef="gm:e.y" />
185            <scalar dataType="xsd:string" dictRef="gm:e.yt" />
186            <scalar dataType="xsd:string" dictRef="gm:e.z" />
187            <scalar dataType="xsd:string" dictRef="gm:e.zt" />
188            <scalar dataType="xsd:string" dictRef="gm:swapcoords">no</scalar>
189            <scalar dataType="xsd:string" dictRef="gm:adress">no</scalar>
190            <scalar dataType="xsd:string" dictRef="gm:user1.grps" />
191            <scalar dataType="xsd:string" dictRef="gm:user2.grps" />
192            <scalar dataType="xsd:string" dictRef="gm:userint1">0</scalar>
193            <scalar dataType="xsd:string" dictRef="gm:userint2">0</scalar>
194            <scalar dataType="xsd:string" dictRef="gm:userint3">0</scalar>
195            <scalar dataType="xsd:string" dictRef="gm:userint4">0</scalar>
196            <scalar dataType="xsd:string" dictRef="gm:userreal1">0</scalar>
197            <scalar dataType="xsd:string" dictRef="gm:userreal2">0</scalar>
198            <scalar dataType="xsd:string" dictRef="gm:userreal3">0</scalar>
199        </module>
200    </comment>

Template definition

1<templateList id="init">  <template name="Input parameters" pattern="\s*\S+\s*=.*" endPattern=".*" endOffset="0" repeat="*">    <record id="r2" repeat="*">\s*{X,gm:name}\s*=\s*{X,gm:value}</record>    <transform process="setValue" xpath="//cml:scalar[@dictRef='gm:name']" value="$string(lower-case(./text()))" />    <transform process="setValue" xpath="//cml:scalar[@dictRef='gm:name']" value="$string(replace(./text(), '[_-]', '.'))" />    <transform process="createNameValue" xpath="./cml:list/cml:list" name="*[@dictRef='gm:name']" value="*[@dictRef='gm:value']" />    <transform process="pullup" xpath="//cml:scalar" repeat="3" />    <transform process="delete" xpath="//cml:module" />
2        </template>
3    </templateList>