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Allink
v0.1
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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] } ...
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
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
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> [ΔL<sup>-2</sup>] LabelY ⟨h<sup>2</sup>⟩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
1.7.6.1