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| | | ####### Vesicle definitions ########### |
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| | | # nshell is a number of divisions of dipyramid |
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| | | <<<<<<< HEAD |
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| | | nshell=17 |
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| | | ======= |
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| | | nshell=10 |
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| | | >>>>>>> nirgov |
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| | | # dmax is the max. bond length (in units l_min) |
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| | | dmax=1.7 |
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| | | # dmin_interspecies in the min. dist. between different vertex species (in units l_min) |
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| | | dmin_interspecies=1.2 |
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| | | # bending rigidity of the membrane (in units kT) |
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| | | xk0=10.0 |
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| | | xk0=20.0 |
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| | | # max step size (in units l_min) |
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| | | stepsize=0.15 |
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| | | |
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| | |
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| | | #Constant area constraint (0 disable constant area, 2 enable constant area with epsarea) |
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| | | constareaswitch=0 |
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| | | |
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| | | #Stretching |
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| | | stretchswitch=0 |
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| | | xkA0=1.0 |
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| | | |
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| | | ####### Polymer (brush) definitions ########### |
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| | | # npoly is a number of polymers attached to npoly distinct vertices on vesicle |
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| | | npoly=800 |
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| | | npoly=0 |
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| | | # nmono is a number of monomers in each polymer |
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| | | nmono=6 |
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| | | nmono=0 |
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| | | # Spring constant between monomers of the polymer |
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| | | k_spring=800 |
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| | | #set to 1 if half of the polymeres are inside the vesicle |
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| | | internal_poly=1 |
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| | | internal_poly=0 |
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| | | |
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| | | ####### Filament (inside the vesicle) definitions ########### |
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| | | # nfil is a number of filaments inside the vesicle |
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| | |
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| | | R_nucleusY=0 |
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| | | R_nucleusZ=0 |
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| | | ####### Cell definitions ############ |
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| | | nxmax=60 |
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| | | nymax=60 |
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| | | nzmax=60 |
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| | | nxmax=100 |
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| | | nymax=100 |
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| | | nzmax=100 |
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| | | |
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| | | |
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| | | ####### Program Control ############ |
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| | |
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| | | mcsweeps=2000 |
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| | | #how many initial mcsweeps*inititer MC sweeps before recording to disk? |
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| | | #2 |
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| | | inititer=10 |
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| | | inititer=0 |
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| | | #how many records do you want on the disk iteration are there in a run? |
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| | | #10000 |
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| | | iterations=100 |
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| | |
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| | | #cuda options??? |
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| | | |
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| | | |
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| | | #NirGov branch only! |
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| | | #number of vertices with spontaneous curvature (integer) |
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| | | number_of_vertices_with_c0=100 |
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| | | #spontaneous curvature (float) |
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| | | number_of_vertices_with_c0=400 |
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| | | #c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float) |
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| | | c0=0.5 |
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| | | #energy of attraction of vertices with spontaneous curvature (float, positive value for attraction) |
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| | | w=10.0 |
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| | | #direct force on vesicles with spontaneous curvature (float) |
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| | | F=2.0 |
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| | | F=0.0 |
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| | | |
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| | | #plane confinement |
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| | | plane_confinement_switch=0 |
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| | | #final plane distance (float in lmin) |
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| | | plane_d=10 |
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| | | #plane to vesicle repulsion force while closing |
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| | | plane_F=10 |
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