input.parameters ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
Template attributes ​
| Attribute | Value |
|---|---|
| source | GROMACS log |
| id | input.parameters |
| name | Input section |
| pattern | Input\sParameters:.* |
| endPattern | \s* |
| endOffset | 1 |
| xml:base | job/input.xml |
Input ​
Input Parameters:
integrator = md
tinit = 0
dt = 0.0005
nsteps = 8000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 10
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 500
nstcalcenergy = 10
nstenergy = 1000
nstxout-compressed = 2000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 40
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 1.7
rlistlong = 1.7
nstcalclr = 10
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.7
epsilon-r = 1
epsilon-rf = 1
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1.7
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.12
fourier-nx = 128
fourier-ny = 128
fourier-nz = 128
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
implicit-solvent = No
gb-algorithm = Still
nstgbradii = 1
rgbradii = 1
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
tcoupl = Berendsen
nsttcouple = 2
nh-chain-length = 0
print-nose-hoover-chain-variables = FALSE
pcoupl = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 2
tau-p = 4
compressibility (3x3):
compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
ref-p (3x3):
ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
QMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = TRUE
Shake-SOR = TRUE
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
interactiveMD = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
simulated-tempering = FALSE
E-x:
n = 0
E-xt:
n = 0
E-y:
n = 0
E-yt:
n = 0
E-z:
n = 0
E-zt:
n = 0
swapcoords = no
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 2027.99 2139.99 563301
ref-t: 300 300 300
tau-t: 0.02 0.1 0.1
annealing: No No No
annealing-npoints: 0 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0 0 0
energygrp-flags[ 1]: 0 0 0
energygrp-flags[ 2]: 0 0 0
Output text ​
xml
<comment class="example.output" id="input.parameters">
<module cmlx:templateRef="input.parameters">
<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: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">10</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:cutoff.scheme">Verlet</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstlist">40</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">FALSE</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">1.7</scalar>
<scalar dataType="xsd:string" dictRef="gm:nstcalclr">10</scalar>
<scalar dataType="xsd:string" dictRef="gm:coulombtype">PME</scalar>
<scalar dataType="xsd:string" dictRef="gm:coulomb.modifier">Potential-shift</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:vdw.type">Cut-off</scalar>
<scalar dataType="xsd:string" dictRef="gm:vdw.modifier">Potential-shift</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:fourierspacing">0.12</scalar>
<scalar dataType="xsd:string" dictRef="gm:fourier.nx">128</scalar>
<scalar dataType="xsd:string" dictRef="gm:fourier.ny">128</scalar>
<scalar dataType="xsd:string" dictRef="gm:fourier.nz">128</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">0</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">2.05016</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">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:print.nose.hoover.chain.variables">FALSE</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</scalar>
<scalar dataType="xsd:string" dictRef="gm:refcoord.scaling">No</scalar>
<matrix cols="3" dataType="xsd:double" dictRef="gm:compressibility" rows="3">4.50000e-05 0.00000e+00 0.00000e+00 0.00000e+00 4.50000e-05 0.00000e+00 0.00000e+00 0.00000e+00 4.50000e-05</matrix>
<matrix cols="3" dataType="xsd:double" dictRef="gm:ref.p" rows="3">1.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 1.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 1.00000e+00</matrix>
<scalar dataType="xsd:string" dictRef="gm:qmmm">FALSE</scalar>
<scalar dataType="xsd:string" dictRef="gm:qmconstraints">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:qmmmscheme">0</scalar>
<scalar dataType="xsd:string" dictRef="gm:mmchargescalefactor">1</scalar>
<array dataType="xsd:double" dictRef="gm:posres.com" size="3">0.00000e+00 0.00000e+00 0.00000e+00</array>
<array dataType="xsd:double" dictRef="gm:posres.comb" size="3">0.00000e+00 0.00000e+00 0.00000e+00</array>
<scalar dataType="xsd:string" dictRef="gm:simulated.tempering">FALSE</scalar>
<matrix cols="3" dataType="xsd:double" dictRef="gm:deform" rows="3">0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00</matrix>
<array dataType="xsd:string" dictRef="gm:nrdf" size="3">2027.99 2139.99 563301</array>
<scalar dataType="xsd:string" dictRef="gm:swapcoords">no</scalar>
<scalar dataType="xsd:string" dictRef="gm:adress">FALSE</scalar>
<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>
<scalar dataType="xsd:string" dictRef="gm:userreal4">0</scalar>
<array dataType="xsd:string" dictRef="gm:ref.t" size="3">300 300 300</array>
<array dataType="xsd:string" dictRef="gm:tau.t" size="3">0.02 0.1 0.1</array>
<array dataType="xsd:string" dictRef="gm:annealing" size="3">No No No</array>
<array dataType="xsd:string" dictRef="gm:annealing.npoints" size="3">0 0 0</array>
<array dataType="xsd:string" dictRef="gm:acc" size="3">0 0 0</array>
<array dataType="xsd:string" dictRef="gm:nfreeze" size="3">N N N</array>
</module>
</comment>Template definition ​
xml
<record />
<template id="discarded" pattern="\s*E-.*" endPattern=".*" endOffset="1">
</template>
<template id="array" pattern="\s*\w.+:\s+\S+.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record>{A,gm:name}:{X,gm:value}</record> <transform process="createArray" xpath=".//cml:scalar[@dictRef='gm:value']" splitter="\s+" from="." /> <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="pullup" xpath=".//cml:scalar" /> <transform process="pullup" xpath=".//cml:array" /> <transform process="addAttribute" xpath=".//cml:array" name="dictRef" value="$string(concat('gm:', ../cml:scalar[@dictRef='gm:name']))" /> <transform process="pullup" xpath=".//cml:array" repeat="2" />
</template>
<template id="single" pattern="\s{3}\w.+=.+" endPattern=".+\(.*\):.*" endPattern2="~" 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" />
</template>
<template id="array" pattern=".+\(\d+\):.*" endPattern=".+\(\d+\):.*" endPattern2=".+\(.+x.+\):.*" endPattern3="\s{1,5}\w.*" endPattern4="~" endOffset="0" repeat="*"> <record>{X,gm:name}\(.*</record> <record repeat="*" makeArray="true">.*={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="pullup" xpath=".//cml:scalar" /> <transform process="pullup" xpath=".//cml:array" /> <transform process="addAttribute" xpath=".//cml:array" name="dataType" value="xsd:double" /> <transform process="addAttribute" xpath=".//cml:array" name="dictRef" value="$string(concat('gm:', parent::cml:module/cml:scalar[@dictRef='gm:name']))" /> <transform process="pullup" xpath=".//cml:array" />
</template>
<template id="matrix" pattern=".+\(.+x.+\):.*" endPattern=".+\(.+x.+\):.*" endPattern2="\s{1,5}\w.*" endPattern3="~" endOffset="0" repeat="*"> <record>{X,gm:name}\(.*</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="pullup" xpath=".//cml:scalar" /> <record repeat="*">.*\{{X,cc:dummy},*\}</record> <transform process="split" xpath=".//cml:scalar[@dictRef='cc:dummy']" splitter=",\s*" /> <transform process="createArray" xpath=".//cml:list[@dictRef='cc:dummy']" from="cml:scalar" /> <transform process="addAttribute" xpath=".//cml:array" name="dataType" value="xsd:double" /> <transform process="createMatrix" xpath="." from=".//cml:array" dictRef="cc:dummy" /> <transform process="pullup" xpath=".//cml:matrix" repeat="2" /> <transform process="addAttribute" xpath=".//cml:matrix" name="dictRef" value="$string(concat('gm:', parent::cml:module/cml:scalar[@dictRef='gm:name']))" /> <transform process="pullup" xpath=".//cml:matrix" />
</template>
<transform process="delete" xpath=".//cml:list" />
<transform process="delete" xpath=".//cml:module" />