Allink  v0.1
Parameter File

ElPoly

Parameter file for the initialisation of a lipid system (used by ElPoly):

#System:
IfSystem 0 #(0) .dat or (1) .xvl format files
#Soft: planar tube di6.0ibuted vesicle
NSoft 1 #number of soft bodies
# Pos Vel Rad Hei Tens type name
#Soft x(0.5 0.5 0.5) v(0.0 0.0 0.0) c(3.0 0.0 1.0) s{vesicle} n{LIPID}
Soft x(0.5 0.5 0.5) v(0.0 0.0 0.0) c(6.0 0.0 1.0) s{planar} n{LIPID}
#Soft x(0.5 0.5 0.5) v(0.0 0.0 0.0) c(6.0 0.0 0.04) s{obstacle} n{LIPID}
#Soft x(0.5 0.5 0.7) v(0.0 0.0 0.0) c(6.0 0.0 1.0) s{planar} n{LIPID2}
#Soft x(0.5 0.5 0.3) v(0.0 0.0 0.0) c(6.0 0.0 1.0) s{planar} n{LIPID2}
Soft x(0.5 0.5 0.5) v(0.0 0.0 0.0) c(5.0 0.0 1.0) s{distributed} n{DISTR}
Soft x(0.5 0.5 0.5) v(0.0 0.0 0.0) c(5.0 0.0 1.5) s{coating} n{VESICLE}
Soft x(0.5 0.5 0.5) v(0.0 0.0 0.0) c(5.0 6.0 1.0) s{tube} n{LIPID}
#Geometry
Lx 12 Ly 12 Lz 14 #box size
CNorm 2 #normal direction
#Additional
NAddChain 0 #number of added chains
NStuffing 0 #number of phil monomers in the peptide
NSolvent 0000 #number of ghost solvent atoms
#Inclusion:
NNano 2 #number of nanoparticles
# RelPos Axis rad str hei coat [no,sph,cyl,wall,cluster,tilt,pore,dip]
#Rigid x(0.5 0.5 0.5) a(0.00 0.00 1.00) c(1.00 1.00 4.00 2.20) s{wall}
Rigid x(0.2 0.5 0.5) a(0.00 0.00 1.00) c(1.00 2.00 5.00 2.20) s{cluster}
Rigid x(0.7 0.5 0.5) a(0.00 0.00 1.00) c(1.00 2.00 5.00 2.20) s{cluster}
#Rigid x(0.5 0.5 0.57) a(1.00 0.00 0.00) c(.50 3.00 12.00 2.20) s{clinks}
#Rigid x(0.5 0.5 0.5) a(1.00 0.00 0.00) c(1.00 2.0 14.00 2.20) s{janus}
Rigid x(0.5 0.5 0.5) a(0.00 0.00 1.00) c(2.00 2000.00 6.00 2.20) s{cluster}
Rigid x(0.6 0.4 0.5) a(0.00 0.00 1.00) c(1.00 2000.00 6.00 2.20) s{cluster}
Rigid x(0.4 0.6 0.5) a(0.00 0.00 1.00) c(1.00 2000.00 6.00 2.20) s{cluster}
Rigid x(0.2 0.8 0.5) a(0.00 0.00 1.00) c(1.00 2000.00 6.00 2.20) s{cluster}
Rigid x(0.5 0.5 .9) a(0.00 0.00 1.00) c(1.0 0.5 2.00 0.0002) s{tip}
#Rigid x(0.5 0.5 .5) a(0.00 0.00 1.00) c(1.0 6.0 12.00 1.00) s{pore}
Rigid x(0.5 0.5 0.25) a(0.00 0.00 1.00) c(.5 1.0 4.00 1.00) s{wall}
Rigid x(0.5 0.5 0.5) a(0.00 0.00 1.00) c(2.0 2.0 6.00 2.20) s{cluster}
#Rigid x(0.5 0.5 0.5) a(0.00 0.00 1.00) c(1.0 6.0 14.00 1.00) s{sph}
Rigid x(0.5 0.5 0.5) a(0.00 0.00 1.00) c(1.00 6.00 10.00 2.20) s{tilt}
Rigid x(0.5 0.5 0.5) a(0.00 0.00 1.00) c(1.00 6.00 10.00 2.20) s{cyl}
NCircle 40 #number of monomer per 0.1ius unity
NHeight 5 #number of monomer per side unity
#Interactions:
chiN 30 #incompatibilty between the species
rho 10 6 #density coexistance
kappaN 70 #rigidity
kappaBend 3. #bending coefficient
kappaSpring 20.537 #spring coefficient
ReOverCutOff 2 #Re/CutOff
vBB 0.1 #Chemical potential of the water
IfTwoTails 0 #construct the lipid with two tails
DiblockLim 8 #number of hydrophilic
NPartPChain 10 #number of beads per chain
WFuncStraight2 .9 #weighting function straight length
WFuncStraight3 1. #weighting function straight length

Example of a system file:

# L=12.000000 12.000000 18.000000 t=0.000000 blocks=2
# v=-24.33 -7.17 -24.33 0.10 -7.17 0.00 w=3.00 3.00 3.00 3.00 3.00 3.00 0.00 3.00 3.00 0.00
# a2=0.9 a3=1.0 Re=2.0 N=10 ks=20.537 kb=3.000 l0=0
# Rigid x(6.00 6.00 9.00) a(0.00 0.00 1.00) c(1.00 1.00 4.00 2.2000) s{wall}
# Rigid x(2.40 2.40 3.60) a(0.00 0.00 1.00) c(1.00 1.00 4.00 2.2000) s{cyl}
# Pep x(6.00 6.00 9.00) a(0.00 0.00 1.00) g(2.00 6.00 2000.00) i[2] d[80 30] fn{Architecture2.dat}
# n=510 N=10 name=LIPID0
11.601412 10.858886 7.173472 0.158991 0.248636 -0.262377 0
11.640605 11.011927 7.639597 0.171554 0.508449 0.081183 0
11.558340 11.027104 7.401688 0.074257 0.331909 -0.188259 0
11.366910 11.415070 7.646884 -0.261508 0.044753 0.115262 0
11.287795 10.646103 7.537098 0.232126 0.155637 0.120164 0
10.660425 10.121575 7.553806 -0.321680 0.239232 0.111970 0
11.034412 10.219047 7.355556 -0.065595 0.134239 0.304619 0
10.496886 9.737709 7.116385 -0.054618 0.079027 0.161831 0
10.134289 9.152025 7.000000 -0.007443 0.177523 -0.165724 1
10.234959 9.188418 6.805128 -0.101392 -0.369108 0.386933 1
...

The same system in an alternative file format:

# l( 12 12 18) c[511] s[0] n[7500] L[6] v[200] d[part] D(0.010000) i(6.00 30.00 70.00)
# Rigid x(6.00 6.00 9.00) a(0.00 0.00 1.00) c(1.00 1.00 4.00 2.2000) s{wall}
# Rigid x(2.40 2.40 3.60) a(0.00 0.00 1.00) c(1.00 1.00 4.00 2.2000) s{cyl}
# Pep x(6.00 6.00 9.00) a(0.00 0.00 1.00) g(2.00 6.00 2000.00) i[2] d[80 30] fn{Architecture2.dat}
{ t[0 0 0] x(1.189071 6.622403 7.549680) v(-0.176953 -0.431976 -0.035858) l[1] }
{ t[1 0 0] x(1.139056 7.032122 7.560085) v(0.081602 0.258855 -0.281085) l[0] l[2] }
{ t[2 0 0] x(1.308140 6.519256 7.442227) v(-0.091691 -0.026668 -0.192819) l[1] l[3] }
{ t[3 0 0] x(1.950485 6.142468 7.036736) v(-0.305010 0.196748 -0.057231) l[2] l[4] }
{ t[4 0 0] x(2.769803 5.534333 7.507009) v(-0.095458 -0.132241 0.174891) l[3] l[5] }
{ t[5 0 0] x(3.094308 5.454964 7.893810) v(0.301184 -0.342642 0.262871) l[4] l[6] }
{ t[6 0 0] x(2.911270 5.487582 7.605564) v(0.021949 0.001945 -0.102675) l[5] l[7] }
{ t[7 0 0] x(2.908146 5.974122 7.503403) v(0.095940 -0.258329 -0.459624) l[6] l[8] }
{ t[8 0 1] x(3.164008 6.124001 7.000000) v(-0.070202 -0.203646 0.363292) l[7] l[9] }
{ t[9 0 1] x(3.663501 5.760973 6.877247) v(-0.163645 0.152836 -0.317551) l[8] }
...

Draw

Parameter file for the visualisation parameters (used by Draw):

Pre 1 #perspective
Passo 10 #number of grid lines
Box 1 #enable the box lines
OffSet 0. 0. 0. #offset position
Rotate -84. 0. 166. #intial rotation
Sun 50. 1045. 0. #sun position
Background 1. 1. 1. #background color
Wheel -1.35 #initial distance
GridEdge 0 0 0 #number of lines per edge
Legend -.4 -.4 0. .4 .8 #position of the legend
Info -.4 -.4 0. #position of the info string

Example of a script for the Draw engine:

#everything is normalized to 1
Arrow
0.0 0.3 0.0 1.0 3.0
0.0 0.0 0.0 1.0 0.0 0.0
Text
height
0.0 0.0 0.0 1.0 3.0
1.1 0.0 -0.05
Polygon #Wall
0.4 0.1 0.1 1.0
0.0 0.0 0.125
1.0 0.0 0.125
1.0 1.0 0.125
0.0 1.0 0.125
Fog #color(3) alpha(1) \\ dens(1) type(1) from(1) boh(2) to(1)
0.0 1.0 0.0 1.0
1 0.35 0.0 0.0 0.0 0.125

Dinamica

Parameter file for a molecuar dynamics simulation (used by Dinamica):

#Sys size/type
NEdge 300 #number of particle per edge/box
Edge 20 20 20 #box size
SysShape md #0d 2d 3d leaves trial rigid mc md
CalcMode NVT #ensemble: NVT NcVT mcVT mVT
Potential LJ #potential: LJ LJ39 Harmonic
PotentialMode DensFunc #Pair DensFunc DensFuncCh
#Dyn quantities
Deltat 0.003 #integration delta t
NChemPotId 200. #eq number of particles
ChemPotEx 0 #interaction energy
Viscosity 0.2 #viscosity parameter
Temp 1 #temperature
#Force parameters
El -1 -1 1265 #elastic coupling
Lap 3 #laplacian prefactor
SLap 0.1 #square laplacian prefactor
Ext 0. #external force
LJ 8.5 #Lennard Jones prefactor
LJMin 1 #Lennard Jones minimum
CutOff 1 #cutoff distance
Cont 0. #contact/friction coefficient
Elong 0.2 0.1 0.2 #rest distance for the armonic spring
#boundary
IncrDist 0.01 #increase the distance of the selected bead
ExtRad .12 #radius of the inclusion
ExtHeight .52 #height of the inclusion
ExtAngle 60. #contact angle
ExtCenter .09 .0 .5 #position of the center
#tension profile
TNSlab 60 #number of slabs
TNDim 3 #number of dimensions
TNComp 6 #number of components
TCalcMode 2d #calculation mode
#visualisation
NOut 1000 #number of points for visualizing the splines
IfMovie 0 #if produces images of the snaphots
IfLine 0 #if draws the line
NUpdate 1000 #how many timesteps before redrawing
IfInterp 0 #if interpolates the points

Parameter file for a Monte Carlo simulation (used by Dinamica):

#Sys size/type
NEdge 300 #number of particle per edge/box
Edge 20 20 20 #box size
SysShape mc #0d 2d 3d leaves trial rigid mc md
CalcMode mcVT #ensemble: NVT NcVT mcVT mVT
Potential LJ #potential: LJ LJ39 Harmonic
PotentialMode DensFuncCh #Pair DensFunc DensFuncCh
SimLimit 100000 #maximum number of timesteps
#Dyn quantities
Deltat 0.003 #integration delta t
NChemPotId 100. #eq number of particles
ChemPotEx 10.5 #ext chem pot (more neg: del,less neg: add)
Viscosity 0.2 #viscosity parameter
Temp 1 #temperature
#Force parameters
El -1 -1 1265 #elastic coupling
Lap 3 #laplacian prefactor
SLap 0.1 #square laplacian prefactor
Ext 0. #external force
LJ 8.5 #Lennard Jones prefactor
LJMin 1 #Lennard Jones minimum
CutOff 1 #cutoff distance
Cont 0. #contact/friction coefficient
Elong 0.2 0.1 0.2 #rest distance for the armonic spring
#boundary
IncrDist 0.01 #increase the distance of the selected bead
ExtRad .12 #radius of the inclusion
ExtHeight .52 #height of the inclusion
ExtAngle 60. #contact angle
ExtCenter .09 .0 .5 #position of the center
#tension profile
TNSlab 60 #number of slabs
TNDim 3 #number of dimensions
TNComp 6 #number of components
TCalcMode 3d #calculation mode
#visualisation
NSpline 1000 #number of points for visualizing the splines
IfMovie 0 #if produces images of the snaphots
IfLine 0 #if draws the line
NUpdate 100 #how many timesteps before redrawing
NWrite 10000 #how many timesteps before writing
IfInterp 0 #if interpolates the points

Parameter file for the solution od a differential equation in 2d (used by Dinamica):

Sys size/type
NEdge 60 #number of particle per edge/box
Edge 30 30 5 #box size
SysShape 2d pore #0d 2d 3d leaves trial rigid mc md
CalcMode NVT #ensemble: NVT NcVT mcVT mVT
Potential LJ #potential: LJ LJ39 Harmonic
PotentialMode DensFunc #Pair DensFunc DensFuncCh
Thermostat no #Langevin
#Dyn quantities
Deltat 0.003 #integration delta t
Viscosity 0.2
ChemPotId 200. #eq number of particles
ChemPotEx 0 #interaction energy
Temp 1 #temperature
#Force parameters
El 1 -1 10000 #elastic coupling
Lap 0.52 #laplacian prefactor
SLap 1 #square laplacian prefactor
Ext 0. #external force
LJ 8.5 #Lennard Jones prefactor
LJMin 1 #Lennard Jones minimum
CutOff 1 #cutoff distance
Cont 0. #contact/friction coefficient
Elong 0.2 0.1 0.05 #rest distance for the armonic spring
#boundary
Rigid x(15. 15. 0.0) a(0.00 0.00 1.00) c(1.0 35.00 2.0 2.2000) s{cyl}
#Rigid x(0.7 0.25 0.5) a(0.00 0.00 1.00) c(0.05 35.00 0.4 2.2000) s{cyl}
Boundary 1 1 1 1 0 0 #boundary conditions on x0 x1 y0 y1 z0 z1
Periodic 1 1 1 #periodic image convention on x y z
#tension profile
TNSlab 60 #number of slabs
TNDim 3 #number of dimensions
TNComp 6 #number of components
TCalcMode 3d #calculation mode
#visualisation
NSplie 1000
NOut 1000 #number of points for visualizing the splines
IfMovie 0 #if produces images of the snaphots
IfLine 0 #if draws the line
NUpdate 1000 #how many timesteps before redrawing
IfInterp 0 #if interpolates the points
NWrite 2000 #how many timesteps before dumping a trajectory file

Visualizza

Script file for the plotting options (used by Visualizza):

# α-a β-b γ-c δ-d ε-e ζ-f η-g θ-h ι-i κ-l λ-k μ-l ν-m ξ-n ο-o π-p ρ-q σ-r ς-r τ-s υ-t φ-u ψ-v ω-x χ-y
# http://htmlhelp.com/reference/html40/entities/symbols.html
NGrid
6 6
#XBound
-90 10
#YBound
5 500
FontSize
32
RatioWidthHeight
1.3
DigPrecX
2 f
DigPrecY
2 f
#ViewportX
0.05
#ViewportY
0.05
LabelX
q<sup>2</sup> [&Delta;L<sup>-2</sup>]
LabelY
&lang;h<sup>2</sup>&rang;L<sup>2</sup> [k<sub>B</sub>T]
#Title
Tension Profile
#ScaleX
1.0
#OffSetX
-9.9
#ScaleY
3.9
PosLegend
.05 .25 .9 .9
PosInterp
.5 .9
Line
1 #number of line
0.7 0.0 0.4 1.0 #color
2 # 0 no line, 1 dots, 2 lines, 3 lines and dots
midplane
Line
2 #number of line
0.0 0.7 0.0 1.0 #color
2 # 0 no line, 1 dots, 2 lines, 3 lines and dots
upper
Line
3 #number of line
0.0 0.0 0.7 1.0 #color
2 # 0 no line, 1 dots, 2 lines, 3 lines and dots
lower
Line
4 #number of line
0.5 0.2 0.7 1.0 #color
2 # 0 no line, 1 dots, 2 lines, 3 lines and dots
thickness
PutStr
0. 0. 0. 1.
.17 .84 0 16
S 1 H 4