dpd

Title	" Carbon Nanotubes in bulk solvent "
Date	30/08/07
Comment	" Is dffusion inside a CNT 1d?  "


State	random


Bead	H
		0.5
    	25	
    	4.5	

Bead	P
		0.5
    	25	25	
    	4.5	4.5	

Bead	T
		0.5
    	25	25	25	
    	4.5 4.5	4.5

Bead	C1
		0.5
		55	55	55	25
		4.5	4.5	4.5	4.5

Bead	C2
		0.5
		55	55	55	55  25
		4.5	4.5	4.5	4.5 4.5

Bead	C3
		0.5
		55	55	55	55  55  25
		4.5	4.5	4.5	4.5 4.5 4.5

Bead	C4
		0.5
		55	55	55	55  55  55  25
		4.5	4.5	4.5	4.5 4.5 4.5 4.5

Bead	C5
		0.5
		55	55	55	55  55  55  55  25
		4.5	4.5	4.5	4.5 4.5 4.5 4.5 4.5

Bead	W
		0.5
		55	55	55	55  55  55  55  25  25
		4.5	4.5	4.5	4.5 4.5 4.5 4.5 4.5 4.5


Bond		H P		64		0.5
Bond		P P		64		0.5
Bond		P T		64		0.5
Bond		C1 C1   256		0.5
Bond		C2 C2   256		0.5
Bond		C3 C3   256		0.5
Bond		C4 C4   256		0.5
Bond		C5 C5   256		0.5

BondPair C1 C1 C1   20.0 0.0
BondPair C2 C2 C2   20.0 0.0
BondPair C3 C3 C3   20.0 0.0
BondPair C4 C4 C4   20.0 0.0
BondPair C5 C5 C5   20.0 0.0

Polymer  Water  1.0  " (W) "
 
Box		32  32  32     1 1 1
Density		3
Temp		1
RNGSeed		-3333
Lambda		0.5
Step		0.005
Time		1000000
SamplePeriod	100
AnalysisPeriod	100000
DensityPeriod	1000000
DisplayPeriod	10000
RestartPeriod	1000000
Grid		1 1 1


Command ToggleBeadDisplay			      1  W
Command SetCurrentStateCamera       1 0.5 -1.0 -1.0   0.5 0.5 0.5

Command SelectPolymerTypeHeadInCylinder   1000  tube1 Water   0 0 1 0.5 0.5 0.5  0.35 4.0 6.0
Command SelectBeadTypeInCylinder          1000  tube1Beads W  0 0 1 0.5 0.5 0.5  0.35 4.0 6.0
Command PolymerisePolymersInTarget        1000  tube1 12 1.0 1.0 64.0 0.5
Command ChangeNamedBeadType               1000  tube1Beads cnt
Command SetTargetDisplayId                1000  tube1  1


Command Comment   1000 // Now create a small sphere inside the tube and measure its diffusion, and make it slightly repelled from the tube  //

Command SelectPolymerTypeHeadInSphere     1000   ball       Water 0.5 0.5 0.5  0.0 2.0
Command SelectBeadTypeInSphere            1000   ballBeads  W     0.5 0.5 0.5  0.0 2.0
Command PolymerisePolymersInTarget        1000   ball       12 1.0 1.0 64.0 0.5
Command ChangeNamedBeadType               1000   ballBeads  b1
Command SetTargetDisplayId                1000   ball       2

Command SetDPDBeadConsInt                 1000   cnt b1  20.0

Command SetTimeStepSize                   2000  0.02