dpd

Title	" BIOENG 455 FRAP experiment "
Date    24/10/22
Comment	" Colour a circular area of lipids in a membraneand measure how they diffuse away over time  "

State	lamella
        Polymer	Lipid
        Normal		0 0 1
        Centre		0.5
        Thickness	5.0
        Linearise	1
        UpperFraction	0.5
        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


Bond      H H  128	0.5
Bond      H T  128	0.5
Bond      T T  128	0.5

BondPair  H T T	15.0	0.0
BondPair  T T T	15.0	0.0

Polymer  Water  0.9802   " (W) "
Polymer  Lipid  0.0198   " (H H (* (T T T T)) H T T T T) "

Box       32 32 32       1  1  1
Density     3
Temp        1
RNGSeed	-221678
Lambda		0.5
Step		0.005
Time           10000
SamplePeriod    100
AnalysisPeriod  5000
DensityPeriod   10000
DisplayPeriod   1000
RestartPeriod   10000
Grid		10 10 10


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

 Command SetTimeStepSize         1000     0.02

Command Comment   1000 //  Next command selects all Beads of type H in a cylinder and changes their colour, then we give them a new name so we can change their interactions  //

Command SelectBeadTypeInCylinder             1000  disk2  H    0 0 1  0.5 0.5 0.5  0.2 0 3
Command ChangeNamedBeadType                  1000  disk2  H3
Command SetBeadDisplayId                     1000  H3  4

Command Comment   1000 //  Next command selects all Beads of type T in a cylinder and changes their colour, also change the name here //

Command SelectBeadTypeInCylinder             1000  disk3  T    0 0 1  0.5 0.5 0.5  0.2 0 3
Command ChangeNamedBeadType                  1000  disk3  T4
Command SetBeadDisplayId                     1000  T4  5

Command Comment   1000 //  Now we set the conservative interactions between H and H3 and T and T4 to 10% repulsive values. This speeds up their diffusion  //

Command SetDPDBeadConsInt  1000 H H3   30
Command SetDPDBeadConsInt  1000 T T4   10

Command RgOfBeadTarget     1000  disk2        rgdisk1  5000 10000
Command RgOfBeadTarget     1000  disk3        rgdisk2  5000 10000