dpd

Title	" BIO-692 Exercises 2021 "
Date    15/03/21
Comment	" Membrane with GFP
        H3(T4)2 lipids. 
        Unstretched bond length of 0.5, k3 = 15
        A/N = 1.2,  1707  lipids check how A/N changes with tail length.  "

State	compositelamella
       Polymers		Lipid  LipidGFP
        Normal			0 0 1
        Centre			0.5
        Thickness		5.0
        Linearise		1
       UpperFraction	        0.5   1.0
       Patches		        0  0
        Polymerise             0

Bead  H
      0.5
      30	
      4.5	

Bead  T
      0.5
      35   10
      4.5  4.5

Bead  W
      0.5
      30   75   25
      4.5  4.5  4.5

Bead  L
      0.5
      25   25   23   25
      4.5  4.5  4.5  4.5

Bead  G
      0.5
      25   25   23   25   25
      4.5  4.5  4.5  4.5  4.5


Bond    H H  128	0.5
Bond    H T  128	0.5
Bond    T T  128	0.5
Bond    H L  128    0.5
Bond    L L  128    0.5
Bond    L G  128    0.5
Bond    G G  128    0.5

BondPair    H T T    15.0   0.0
BondPair    T T T    15.0   0.0
BondPair    G G G   20.0   0.0

Polymer  Water    0.977967   " (W) "
Polymer Lipid     0.021993   " (H H (* (T T T T)) H T T T T) "
Polymer LipidGFP  0.000040   " (H (* (L  (* ( G (/ 2 G) G (/ 3 G) G (/ 1 G) ))
(* ( G (/ 2 G) G (/ 3 G) G (/ 1 G) ))
(* ( G (/ 2 G) G (/ 3 G) G (/ 1 G) ))
(* ( G (/ 2 G) G (/ 3 G) G (/ 1 G) ))
(* ( G (/ 2 G) G (/ 3 G) G (/ 1 G) ))
(* ( G (/ 2 G) G (/ 3 G) G (/ 1 G) ))
( G (/ 2 G) G (/ 3 G) G (/ 1 G)
))) H (* (T T T T)) H T T T T) "

Box       32 32 32       1  1  1
Density        3
Temp           1
RNGSeed        -319822
Lambda		0.5
Step		0.005
Time		10000
SamplePeriod     100
AnalysisPeriod	 10000
DensityPeriod    10000
DisplayPeriod    100
RestartPeriod    10000
Grid		1  1  1


Command ToggleBeadDisplay              1    W
Command SetCurrentStateCamera          1    0.5 -0.5 -0.5  0.5 0.5 0.5

Command SetTimeStepSize     1000     0.01