From 6487a03362d35589c286d0660eba123a7ab00535 Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Mon, 10 May 2021 11:14:04 +0000 Subject: [PATCH] Raj and Yoav session in making multiple protein species --- src/tape | 63 ++++++++++++++++++++++++++----- 1 files changed, 52 insertions(+), 11 deletions(-) diff --git a/src/tape b/src/tape index 0801375..f30ddaa 100644 --- a/src/tape +++ b/src/tape @@ -1,6 +1,6 @@ ####### Vesicle definitions ########### # nshell is a number of divisions of dipyramid -nshell=17 +nshell=7 # dmax is the max. bond length (in units l_min) dmax=1.7 # dmin_interspecies in the min. dist. between different vertex species (in units l_min) @@ -14,48 +14,70 @@ # (pswitch=1: calc. p*dV energy contribution) pswitch = 0 # pressure difference: p_inside - p_outside (in units kT/l_min^3): -pressure=0.0 +pressure=10.0 + +#Constant volume constraint (0 disable constant volume, 1 enable wiht additional vertex move, 2 enable with epsvol) +constvolswitch=0 +constvolprecision=1e-14 + +#Constant area constraint (0 disable constant area, 2 enable constant area with epsarea) +constareaswitch=0 + + +#Stretching +stretchswitch=0 +xkA0=1.0 ####### Polymer (brush) definitions ########### # npoly is a number of polymers attached to npoly distinct vertices on vesicle npoly=0 # nmono is a number of monomers in each polymer -nmono=10 +nmono=0 # Spring constant between monomers of the polymer k_spring=800 +#set to 1 if half of the polymeres are inside the vesicle +internal_poly=0 ####### Filament (inside the vesicle) definitions ########### # nfil is a number of filaments inside the vesicle nfil=0 # nfono is a number of monomers in each filament -nfono=300 +nfono=3 # Persistence lenght of the filaments (in units l_min) -xi=0 +xi=100 ####### Nucleus (inside the vesicle) ########### # Radius of an impenetrable hard sphere inside the vesicle R_nucleus=0 - +R_nucleusX=0 +R_nucleusY=0 +R_nucleusZ=0 ####### Cell definitions ############ -nxmax=60 -nymax=60 -nzmax=60 +nxmax=100 +nymax=100 +nzmax=100 ####### Program Control ############ #how many MC sweeps between subsequent records of states to disk -mcsweeps=2500 +#200000 +mcsweeps=200 #how many initial mcsweeps*inititer MC sweeps before recording to disk? +#2 inititer=0 #how many records do you want on the disk iteration are there in a run? -iterations=15000 +#10000 +iterations=10 ###### Spherical harmonics ########### +# If 0 then spherical harmonics are not calculated at all. spherical_harmonics_coefficients=21 #shut up if we are using cluster!!! quiet=false + + #what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto) #currently only none makes sense. @@ -67,3 +89,22 @@ #max number of processes in distributed (voluntary) environment distributed_processes=50 #cuda options??? + + +#number of vertices with spontaneous curvature (integer) +number_of_vertices_with_c0=200 +#c0/2 is spontaneous curvature. c0 is used as (c1+c1-c0)^2 in energy term (float) +c0=1.0 +#energy of attraction of vertices with spontaneous curvature (float, positive value for attraction) +w=10.0 +#direct force on vesicles with spontaneous curvature (float) +F=2.0 + + + +#plane confinement +plane_confinement_switch=0 +#final plane distance (float in lmin) +plane_d=10 +#plane to vesicle repulsion force while closing +plane_F=10 -- Gitblit v1.9.3