dpd

Title	" Sphingomyelin bilayer "
Date    06/01/11
Comment	" Spider venon project - test run of lipids to see what kind of bilayer they form. 
          A/N = not calculated 
		  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 sv16l4 larger box and same A/N.
		  
		  "

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


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

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  0.98787   " (W) "
Polymer	Lipid  0.01213   " (PO4 (* (COH T T T T)) NHO T T T) "

Box       48  48  48      1  1  1
Density		3
Temp        1
RNGSeed		-5477
Lambda		0.5
Step		0.005
Time		100000
SamplePeriod     100
AnalysisPeriod	 100000
DensityPeriod    100000
DisplayPeriod    1000
RestartPeriod    100000
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    1  3.0  2.0

Command SetTimeStepSize     1000     0.02