dpd Title " A proteins binding to a DNA strand " Date 11/03/24 Comment " DNA and the TFs are constrcuted by tying water beads together with Hookean springs at selected locations in the simulation box. Hence, the only polymer type in the box is initially water. FOr this execise, ignore any references to B peptides in this input file. Each run will take approximately 3 days on a single core. The number of TFs created is set by the command on line 185 as a result of the command "ExecuteCommandGroupSequence" which currently says to create 100 TFs. If you change the 100 on that line to a smaller number, it will create fewer TFs. You cannot change it bigger without modifying other commands. See me :-) " State random Bead W 0.5 25 4.5 Bead E 0.5 25 6 4.5 4.5 Bead B 0.5 23 25 25 4.5 4.5 4.5 Bead F 0.5 25 6 25 6 4.5 4.5 4.5 4.5 Bond E E 128 0.5 Bond B B 128 0.5 Bond E B 128 0.5 Bond F F 128 0.5 Bond F B 128 0.5 BondPair B B B 5.0 0.0 Polymer Water 1.0 " (W) " Box 64 64 24 1 1 1 Density 3 Temp 1 RNGSeed -12199 Lambda 0.5 Step 0.01 Time 500000 SamplePeriod 100 AnalysisPeriod 500000 DensityPeriod 500000 DisplayPeriod 5000 RestartPeriod 500000 Grid 1 1 1 Command ToggleBeadDisplay 1 W Command SetCurrentStateCamera 1 0.5 -1.0 -0.5 0.5 0.5 0.5 Command SetCurrentStateDefaultFormat 1 Paraview Command Comment 2000 // Make the DNA next in the centre of the box, aligned with Y axis // Command SelectBeadTypeInCylinder 2000 DNAbeads W 0 1 0 0.5 0.5 0.5 0.5 0 1.5 Command SelectPolymerTypeHeadInCylinder 2000 DNA Water 0 1 0 0.5 0.5 0.5 0.5 0 1.5 Command PolymerisePolymersInTarget 2000 DNA 12 1.5 1.0 32 0.5 Command ChangeNamedBeadType 2000 DNAbeads db Command SetTargetDisplayId 2000 DNAbeads 4 Command Comment 2000 // Now create the rigid cylindrical A peptides just above the DNA. The peptide has three regions, one end is attractive to DNA, the other end to the B peptides, and the middle to itself. // Command CreateCommandGroup 2000 createQD Command AddCommandToGroup 2000 createQD SelectBeadTypeInCylinder var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 Command AddCommandToGroup 2000 createQD SelectPolymerTypeHeadInCylinder var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 Command AddCommandToGroup 2000 createQD CountBeadTypeInTarget var1 var2 Command AddCommandToGroup 2000 createQD PolymerisePolymersInTarget var1 var2 var3 var4 var5 var6 Command AddCommandToGroup 2000 createQD ChangeNamedBeadType var1 var2 Command AddCommandToGroup 2000 createQD SetTargetDisplayId var1 var2 Command AddCommandToGroup 2000 createQD SelectBeadTypeInSlice var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 Command AddCommandToGroup 2000 createQD ChangeNamedBeadType var1 var2 Command AddCommandToGroup 2000 createQD SetTargetDisplayId var1 var2 Command AddCommandToGroup 2000 createQD SelectBeadTypeInSlice var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 Command AddCommandToGroup 2000 createQD ChangeNamedBeadType var1 var2 Command AddCommandToGroup 2000 createQD SetTargetDisplayId var1 var2 Command AddCommandToGroup 2000 createQD SetDPDBeadConsInt var1 var2 var3 Command AddCommandToGroup 2000 createQD SetDPDBeadConsInt var1 var2 var3 Command AddCommandToGroup 2000 createQD SetDPDBeadConsInt var1 var2 var3 Command SetArgumentToStringSequence 2000 createQD 1 var1 Abeads Command SetArgumentToStringConstant 2000 createQD 1 var2 W Command SetArgumentToIntegerConstant 2000 createQD 1 var3 0 Command SetArgumentToIntegerConstant 2000 createQD 1 var4 0 Command SetArgumentToIntegerConstant 2000 createQD 1 var5 1 Command SetArgumentToRealConstant 2000 createQD 1 var9 0.125 Command SetArgumentToRealConstant 2000 createQD 1 var10 0.0 Command SetArgumentToRealConstant 2000 createQD 1 var11 1.0 Command SetArgumentsTo3dRectangularLatticeVector 2000 createQD 1 var6 1 var7 1 var8 10 10 1 0.1 0.1 0.75 0.08 0.08 0.1 Command SetArgumentToStringSequence 2000 createQD 2 var1 Apeptide Command SetArgumentToStringConstant 2000 createQD 2 var2 Water Command SetArgumentToArgument 2000 createQD 2 var3 1 var3 Command SetArgumentToArgument 2000 createQD 2 var4 1 var4 Command SetArgumentToArgument 2000 createQD 2 var5 1 var5 Command SetArgumentToArgument 2000 createQD 2 var6 1 var6 Command SetArgumentToArgument 2000 createQD 2 var7 1 var7 Command SetArgumentToArgument 2000 createQD 2 var8 1 var8 Command SetArgumentToArgument 2000 createQD 2 var9 1 var9 Command SetArgumentToArgument 2000 createQD 2 var10 1 var10 Command SetArgumentToArgument 2000 createQD 2 var11 1 var11 Command SetArgumentToArgument 2000 createQD 3 var1 1 var1 Command SetArgumentToIntegerConstant 2000 createQD 3 var2 3 Command SetArgumentToArgument 2000 createQD 4 var1 2 var1 Command SetArgumentToIntegerConstant 2000 createQD 4 var2 12 Command SetArgumentToRealConstant 2000 createQD 4 var3 1.5 Command SetArgumentToRealConstant 2000 createQD 4 var4 1.0 Command SetArgumentToRealConstant 2000 createQD 4 var5 128.0 Command SetArgumentToRealConstant 2000 createQD 4 var6 0.5 Command SetArgumentToArgument 2000 createQD 5 var1 1 var1 Command SetArgumentToStringSequence 2000 createQD 5 var2 AASite Command SetArgumentToArgument 2000 createQD 6 var1 1 var1 Command SetArgumentToIntegerConstant 2000 createQD 6 var2 5 Command SetArgumentToStringSequence 2000 createQD 7 var1 ADNASite Command SetArgumentToArgument 2000 createQD 7 var2 5 var2 Command SetArgumentToIntegerConstant 2000 createQD 7 var3 0 Command SetArgumentToIntegerConstant 2000 createQD 7 var4 0 Command SetArgumentToIntegerConstant 2000 createQD 7 var5 1 Command SetArgumentToArgument 2000 createQD 7 var6 1 var6 Command SetArgumentToArgument 2000 createQD 7 var7 1 var7 Command SetArgumentToRealConstant 2000 createQD 7 var8 0.7 Command SetArgumentToRealConstant 2000 createQD 7 var9 0.025 Command SetArgumentToRealConstant 2000 createQD 7 var10 0.025 Command SetArgumentToArgument 2000 createQD 7 var11 1 var9 Command SetArgumentToArgument 2000 createQD 8 var1 7 var1 Command SetArgumentToStringSequence 2000 createQD 8 var2 ADNABeads Command SetArgumentToArgument 2000 createQD 9 var1 7 var1 Command SetArgumentToIntegerConstant 2000 createQD 9 var2 6 Command SetArgumentToStringSequence 2000 createQD 10 var1 ABSite Command SetArgumentToArgument 2000 createQD 10 var2 8 var2 Command SetArgumentToIntegerConstant 2000 createQD 10 var3 0 Command SetArgumentToIntegerConstant 2000 createQD 10 var4 0 Command SetArgumentToIntegerConstant 2000 createQD 10 var5 1 Command SetArgumentToArgument 2000 createQD 10 var6 1 var6 Command SetArgumentToArgument 2000 createQD 10 var7 1 var7 Command SetArgumentToRealConstant 2000 createQD 10 var8 0.525 Command SetArgumentToRealConstant 2000 createQD 10 var9 0.025 Command SetArgumentToRealConstant 2000 createQD 10 var10 0.025 Command SetArgumentToArgument 2000 createQD 10 var11 1 var9 Command SetArgumentToArgument 2000 createQD 11 var1 10 var1 Command SetArgumentToStringSequence 2000 createQD 11 var2 ABBeads Command SetArgumentToArgument 2000 createQD 12 var1 10 var1 Command SetArgumentToIntegerConstant 2000 createQD 12 var2 7 Command Comment 2000 // Now set the interactions to the peptides are attracted to dna and themselves. // Command SetArgumentToArgument 2000 createQD 13 var1 5 var2 Command SetArgumentToStringConstant 2000 createQD 13 var2 db Command SetArgumentToRealConstant 2000 createQD 13 var3 15.0 Command SetArgumentToArgument 2000 createQD 14 var1 11 var2 Command SetArgumentToArgument 2000 createQD 14 var2 11 var2 Command SetArgumentToRealConstant 2000 createQD 14 var3 15.0 Command SetArgumentToArgument 2000 createQD 15 var1 11 var2 Command SetArgumentToStringConstant 2000 createQD 15 var2 E Command SetArgumentToRealConstant 2000 createQD 15 var3 6.0 Command ExecuteCommandGroupSequence 2000 createQD 100 1