gromacs.input¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| 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
<comment class="example.output" id="gromacs.input">
<module id="gromacs.input">
<scalar dataType="xsd:string" dictRef="gm:include">-I../top</scalar>
<scalar dataType="xsd:string" dictRef="gm:define" />
<scalar dataType="xsd:string" dictRef="gm:integrator">md</scalar>
<scalar dataType="xsd:string" dictRef="gm:tinit">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:dt">0.0005</scalar>
<scalar dataType="xsd:string" dictRef="gm:nsteps">8000000</scalar>
<scalar dataType="xsd:string" dictRef="gm:init.step">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:simulation.part">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:comm.mode">Linear</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstcomm">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:comm.grps" />
<scalar dataType="xsd:string" dictRef="gm:bd.fric">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:ld.seed">1993</scalar>
<scalar dataType="xsd:string" dictRef="gm:emtol">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:emstep">0.01</scalar>
<scalar dataType="xsd:string" dictRef="gm:niter">20</scalar>
<scalar dataType="xsd:string" dictRef="gm:fcstep">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstcgsteep">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:nbfgscorr">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:rtpi">0.05</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstxout">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstvout">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstfout">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstlog">500</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstcalcenergy">-1</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstenergy">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstxout.compressed">2000</scalar>
<scalar dataType="xsd:string" dictRef="gm:compressed.x.precision">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:compressed.x.grps">LIG COT TBA</scalar>
<scalar dataType="xsd:string" dictRef="gm:energygrps">LIG COT TBA</scalar>
<scalar dataType="xsd:string" dictRef="gm:cutoff.scheme">Verlet</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstlist">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:ns.type">grid</scalar>
<scalar dataType="xsd:string" dictRef="gm:pbc">xyz</scalar>
<scalar dataType="xsd:string" dictRef="gm:periodic.molecules">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:verlet.buffer.tolerance">0.005</scalar>
<scalar dataType="xsd:string" dictRef="gm:rlist">1.7</scalar>
<scalar dataType="xsd:string" dictRef="gm:rlistlong">-1</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstcalclr">-1</scalar>
<scalar dataType="xsd:string" dictRef="gm:coulombtype">PME</scalar>
<scalar dataType="xsd:string" dictRef="gm:coulomb.modifier">Potential-shift-Verlet</scalar>
<scalar dataType="xsd:string" dictRef="gm:rcoulomb.switch">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:rcoulomb">1.7</scalar>
<scalar dataType="xsd:string" dictRef="gm:epsilon.r">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:epsilon.rf">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:vdwtype">cut-off</scalar>
<scalar dataType="xsd:string" dictRef="gm:vdw.modifier">Potential-shift-Verlet</scalar>
<scalar dataType="xsd:string" dictRef="gm:rvdw.switch">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:rvdw">1.7</scalar>
<scalar dataType="xsd:string" dictRef="gm:dispcorr">EnerPres</scalar>
<scalar dataType="xsd:string" dictRef="gm:table.extension">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:energygrp.table" />
<scalar dataType="xsd:string" dictRef="gm:fourierspacing">0.12</scalar>
<scalar dataType="xsd:string" dictRef="gm:fourier.nx">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:fourier.ny">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:fourier.nz">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:pme.order">4</scalar>
<scalar dataType="xsd:string" dictRef="gm:ewald.rtol">1e-05</scalar>
<scalar dataType="xsd:string" dictRef="gm:ewald.rtol.lj">0.001</scalar>
<scalar dataType="xsd:string" dictRef="gm:lj.pme.comb.rule">Geometric</scalar>
<scalar dataType="xsd:string" dictRef="gm:ewald.geometry">3d</scalar>
<scalar dataType="xsd:string" dictRef="gm:epsilon.surface">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:implicit.solvent">No</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.algorithm">Still</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstgbradii">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:rgbradii">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.epsilon.solvent">80</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.saltconc">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.obc.alpha">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.obc.beta">0.8</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.obc.gamma">4.85</scalar>
<scalar dataType="xsd:string" dictRef="gm:gb.dielectric.offset">0.009</scalar>
<scalar dataType="xsd:string" dictRef="gm:sa.algorithm">Ace-approximation</scalar>
<scalar dataType="xsd:string" dictRef="gm:sa.surface.tension">-1</scalar>
<scalar dataType="xsd:string" dictRef="gm:tcoupl">Berendsen</scalar>
<scalar dataType="xsd:string" dictRef="gm:nsttcouple">2</scalar>
<scalar dataType="xsd:string" dictRef="gm:nh.chain.length">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:print.nose.hoover.chain.variables">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:tc.grps">COT TBA LIG</scalar>
<scalar dataType="xsd:string" dictRef="gm:tau.t">0.02 0.1 0.1</scalar>
<scalar dataType="xsd:string" dictRef="gm:ref.t">300 300 300</scalar>
<scalar dataType="xsd:string" dictRef="gm:pcoupl">Parrinello-Rahman</scalar>
<scalar dataType="xsd:string" dictRef="gm:pcoupltype">Isotropic</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstpcouple">2</scalar>
<scalar dataType="xsd:string" dictRef="gm:tau.p">4.0</scalar>
<scalar dataType="xsd:string" dictRef="gm:compressibility">4.5e-5</scalar>
<scalar dataType="xsd:string" dictRef="gm:ref.p">1.0</scalar>
<scalar dataType="xsd:string" dictRef="gm:refcoord.scaling">No</scalar>
<scalar dataType="xsd:string" dictRef="gm:qmmm">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:qmmm.grps" />
<scalar dataType="xsd:string" dictRef="gm:qmmethod" />
<scalar dataType="xsd:string" dictRef="gm:qmmmscheme">normal</scalar>
<scalar dataType="xsd:string" dictRef="gm:qmbasis" />
<scalar dataType="xsd:string" dictRef="gm:qmcharge" />
<scalar dataType="xsd:string" dictRef="gm:qmmult" />
<scalar dataType="xsd:string" dictRef="gm:sh" />
<scalar dataType="xsd:string" dictRef="gm:casorbitals" />
<scalar dataType="xsd:string" dictRef="gm:caselectrons" />
<scalar dataType="xsd:string" dictRef="gm:saon" />
<scalar dataType="xsd:string" dictRef="gm:saoff" />
<scalar dataType="xsd:string" dictRef="gm:sasteps" />
<scalar dataType="xsd:string" dictRef="gm:mmchargescalefactor">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:bopt" />
<scalar dataType="xsd:string" dictRef="gm:bts" />
<scalar dataType="xsd:string" dictRef="gm:annealing" />
<scalar dataType="xsd:string" dictRef="gm:annealing.npoints" />
<scalar dataType="xsd:string" dictRef="gm:annealing.time" />
<scalar dataType="xsd:string" dictRef="gm:annealing.temp" />
<scalar dataType="xsd:string" dictRef="gm:gen.vel">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:gen.temp">300</scalar>
<scalar dataType="xsd:string" dictRef="gm:gen.seed">173529</scalar>
<scalar dataType="xsd:string" dictRef="gm:constraints">all-bonds</scalar>
<scalar dataType="xsd:string" dictRef="gm:constraint.algorithm">Lincs</scalar>
<scalar dataType="xsd:string" dictRef="gm:continuation">yes</scalar>
<scalar dataType="xsd:string" dictRef="gm:shake.sor">yes</scalar>
<scalar dataType="xsd:string" dictRef="gm:shake.tol">0.0001</scalar>
<scalar dataType="xsd:string" dictRef="gm:lincs.order">4</scalar>
<scalar dataType="xsd:string" dictRef="gm:lincs.iter">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:lincs.warnangle">30</scalar>
<scalar dataType="xsd:string" dictRef="gm:morse">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:energygrp.excl" />
<scalar dataType="xsd:string" dictRef="gm:nwall">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:wall.type">9-3</scalar>
<scalar dataType="xsd:string" dictRef="gm:wall.r.linpot">-1</scalar>
<scalar dataType="xsd:string" dictRef="gm:wall.atomtype" />
<scalar dataType="xsd:string" dictRef="gm:wall.density" />
<scalar dataType="xsd:string" dictRef="gm:wall.ewald.zfac">3</scalar>
<scalar dataType="xsd:string" dictRef="gm:pull">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:rotation">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:imd.group" />
<scalar dataType="xsd:string" dictRef="gm:disre">No</scalar>
<scalar dataType="xsd:string" dictRef="gm:disre.weighting">Conservative</scalar>
<scalar dataType="xsd:string" dictRef="gm:disre.mixed">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:disre.fc">1000</scalar>
<scalar dataType="xsd:string" dictRef="gm:disre.tau">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstdisreout">100</scalar>
<scalar dataType="xsd:string" dictRef="gm:orire">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:orire.fc">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:orire.tau">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:orire.fitgrp" />
<scalar dataType="xsd:string" dictRef="gm:nstorireout">100</scalar>
<scalar dataType="xsd:string" dictRef="gm:free.energy">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:couple.moltype" />
<scalar dataType="xsd:string" dictRef="gm:couple.lambda0">vdw-q</scalar>
<scalar dataType="xsd:string" dictRef="gm:couple.lambda1">vdw-q</scalar>
<scalar dataType="xsd:string" dictRef="gm:couple.intramol">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:init.lambda">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:init.lambda.state">-1</scalar>
<scalar dataType="xsd:string" dictRef="gm:delta.lambda">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstdhdl">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:fep.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:mass.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:coul.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:vdw.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:bonded.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:restraint.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:temperature.lambdas" />
<scalar dataType="xsd:string" dictRef="gm:calc.lambda.neighbors">1</scalar>
<scalar dataType="xsd:string" dictRef="gm:init.lambda.weights" />
<scalar dataType="xsd:string" dictRef="gm:dhdl.print.energy">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:sc.alpha">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:sc.power">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:sc.r.power">6</scalar>
<scalar dataType="xsd:string" dictRef="gm:sc.sigma">0.3</scalar>
<scalar dataType="xsd:string" dictRef="gm:sc.coul">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:separate.dhdl.file">yes</scalar>
<scalar dataType="xsd:string" dictRef="gm:dhdl.derivatives">yes</scalar>
<scalar dataType="xsd:string" dictRef="gm:dh.hist.size">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:dh.hist.spacing">0.1</scalar>
<scalar dataType="xsd:string" dictRef="gm:acc.grps" />
<scalar dataType="xsd:string" dictRef="gm:accelerate" />
<scalar dataType="xsd:string" dictRef="gm:freezegrps" />
<scalar dataType="xsd:string" dictRef="gm:freezedim" />
<scalar dataType="xsd:string" dictRef="gm:cos.acceleration">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:deform" />
<scalar dataType="xsd:string" dictRef="gm:simulated.tempering">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:simulated.tempering.scaling">geometric</scalar>
<scalar dataType="xsd:string" dictRef="gm:sim.temp.low">300</scalar>
<scalar dataType="xsd:string" dictRef="gm:sim.temp.high">300</scalar>
<scalar dataType="xsd:string" dictRef="gm:e.x" />
<scalar dataType="xsd:string" dictRef="gm:e.xt" />
<scalar dataType="xsd:string" dictRef="gm:e.y" />
<scalar dataType="xsd:string" dictRef="gm:e.yt" />
<scalar dataType="xsd:string" dictRef="gm:e.z" />
<scalar dataType="xsd:string" dictRef="gm:e.zt" />
<scalar dataType="xsd:string" dictRef="gm:swapcoords">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:adress">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:user1.grps" />
<scalar dataType="xsd:string" dictRef="gm:user2.grps" />
<scalar dataType="xsd:string" dictRef="gm:userint1">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:userint2">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:userint3">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:userint4">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:userreal1">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:userreal2">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:userreal3">0</scalar>
</module>
</comment>
Template definition
<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" />
</template>
</templateList>