dpd

Title	" Sphingomyelin bilayer "
Date    21/01/11
Comment	" Spider venom project - test run of lipids to see what kind of bilayer they form. 
          A/N = 1.7, a tense membrane.
		  The first task is to assign conservative interaction parameters to each bead type. This should incorporate their ability to H-bond to water, 
		  their bulkiness, etc. Here are my first guesses:
		  Chol-Chol  - bulky headgroup so self-interaction is larger than others
		  Chol-Water - neutral
		  Chol-PO4   - neutral
		  Chol-X     - slightly repulsive
		  
		  PO4-PO4    - neutral
		  PO4-Water  - slightly attractive
		  PO4-COH    - neutral
		  PO4-NHO    - neutral
		  
		  T-T        - neutral
		  T-Water    - very repulsive
		  T-PO4      - very repulsive
		  T-COH      - repulsive
		  T-NHO      - repulsive
		  
		  AG params for H, T, W
		  
		  As sv31 but distinct molecules in the upper and lower leaflets and only the upper leaflet has charged PO4. 
		  
		  "

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

Bead  Chol
      0.5
      30
      4.5	

Bead  PO4
      0.5
      30  10
      4.5 4.5

Bead  COH
      0.5
      25	10	 10
      4.5	4.5	 4.5

Bead  NHO
      0.5
      25	10	 10    10
      4.5	4.5	 4.5   4.5

Bead  T
      0.5
      35	35	 30    30    10
      4.5	4.5	 4.5   4.5   4.5

Bead  W
      0.5
      30	30	 25    25    75    25
      4.5	4.5	 4.5   4.5   4.5   4.5
	  
Bead  CPO4
      0.5
	  30   10   10   10   35   30   10
	  4.5  4.5  4.5  4.5  4.5  4.5  4.5


Bond    Chol  PO4   128  0.5
Bond    PO4   COH   128  0.5
Bond    PO4   NHO   128  0.5
Bond    COH   T     128  0.5
Bond    NHO   T     128  0.5
Bond    T     T     128  0.5

Bond    Chol  CPO4   128  0.5
Bond    CPO4   COH   128  0.5
Bond    CPO4   NHO   128  0.5


BondPair	COH T T  15.0  0.0
BondPair	NHO T T  15.0  0.0
BondPair	T   T T  15.0  0.0

Polymer	Water         0.991   " (W) "
Polymer	Lipid         0.0045   " (PO4 (* (COH T T T T)) NHO T T T) "
Polymer	ChargedLipid  0.0045   " (CPO4 (* (COH T T T T)) NHO T T T) "

Box       48  48  48      1  1  1
Density		3
Temp        1
RNGSeed		-92134
Lambda		0.5
Step		0.005
Time		200000
SamplePeriod     100
AnalysisPeriod	 200000
DensityPeriod    200000
DisplayPeriod    1000
RestartPeriod    200000
Grid		1  1  1


Command	ToggleBeadDisplay       1    W
Command SetCurrentStateCamera   1    0.5 -0.5 -0.5  0.5 0.5 0.5
Command SetCurrentStateDefaultFormat  1    Paraview

Command ChargeBeadByType        1    6  4.5  1.4

Command SetTimeStepSize     1000     0.02