dpd

Title    " BIOENG-455 Exercises 2022 "
Date    29/08/22
Comment	" Pulling a single lipid out of a membrane  "

State	compositelamella
       Polymers	Lipid  Lipid1
       Normal		0 0 1
       Centre		0.5
       Thickness	5.0
       Linearise	1
       UpperFraction	0.5  1
       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  H1
      0.5
      30    35    30   30
      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    H1 H  128   0.5

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

Polymer Water   0.978967   " (W) "
Polymer Lipid   0.021013   " (H H (* (T T T T)) H T T T T) "
Polymer Lipid1  0.00002    " (H1 H (* (T T T T)) H T T T T) "

Box       32 32 32       1  1  1
Density	    3
Temp        1
RNGSeed    -3198
Lambda		0.5
Step		0.02
Time		2000
SamplePeriod     10
AnalysisPeriod   2000
DensityPeriod    2000
DisplayPeriod    100
RestartPeriod    2000
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 Comment   1 // Following commands apply a force upwards to the single lipid with the H1 bead  //

Command SelectBeadTypeInSimBox        1  head  H1
Command SelectPolymerTypeInSimBox     1  labelledLipid  Lipid1
Command CountBeadsInTarget            1  head

Command ConstantForceOnTarget         1000  head  fh   0 0 1   1.0

Command DistanceMovedByTarget         1000  head fh  dm1  1000 1200 
Command ExternalWorkOnTarget          1000  head fh  ew1  1000 1200

Command MSDOfPolymerTarget            1000  labelledLipid  msd1 1000 1200

Command RemoveCommandTargetActivity   1200   fh