#################### # QwikMD Input File # # # # # # # # # # #################### set QWIKMD::nucleicmcr {(not name QWIKMDDELETE and nucleic)} set QWIKMD::proteinmcr {(not name QWIKMDDELETE and protein or (resname LYR))} set QWIKMD::heteromcr {(not name QWIKMDDELETE and hetero and not qwikmd_protein and not qwikmd_lipid and not qwikmd_nucleic and not qwikmd_glycan and not water)} set QWIKMD::glycanmcr {(not name QWIKMDDELETE and glycan)} set QWIKMD::lipidmcr {(not name QWIKMDDELETE and lipid)} atomselect macro qwikmd_protein $QWIKMD::proteinmcr atomselect macro qwikmd_nucleic $QWIKMD::nucleicmcr atomselect macro qwikmd_glycan $QWIKMD::glycanmcr atomselect macro qwikmd_lipid $QWIKMD::lipidmcr atomselect macro qwikmd_hetero $QWIKMD::heteromcr $QWIKMD::topGui.nbinput select 0 set QWIKMD::prepared 1 QWIKMD::changeMainTab $QWIKMD::topGui.nbinput.f1.nb select 1 QWIKMD::ChangeMdSmd 1 set aux "[file rootname $QWIKMD::basicGui(workdir,0)]" set QWIKMD::outPath ${aux} cd ${QWIKMD::outPath}/run/ set QWIKMD::inputstrct {Deca-alanine_QwikMD.psf Deca-alanine_QwikMD.pdb} QWIKMD::LoadButt {Deca-alanine_QwikMD.psf Deca-alanine_QwikMD.pdb} array set QWIKMD::basicGui {live 0 currenttime,3 {Simulation time: 0.002 of 10.000 ns} currenttime {Completed 0.000 of 0.000 ns} plength 20 desktop {} temperature,0 27 temperature,1 27 saltconc,0 0.15 scheme {VMD Classic} mdPrec,0 0 pspeed 1 saltions,0 NaCl mdtime,0 10.0 mdtime,1 20.0 currenttime,0 {} currenttime,1 {} solvent,0 Implicit } array set QWIKMD::advGui {live 0 currenttime,3 {Simulation time: 0.002 of 10.000 ns} currenttime {Completed 0.000 of 0.000 ns} plength 20 desktop {} temperature,0 27 temperature,1 27 saltconc,0 0.15 scheme {VMD Classic} mdPrec,0 0 pspeed 1 saltions,0 NaCl mdtime,0 10.0 mdtime,1 20.0 currenttime,0 {} currenttime,1 {} solvent,0 Implicit addmol 10 protocoltb,SMD,1,restrIndex {} protocoltb,MD,0 Minimization membrane,efect translate protocoltb,MD,1 Annealing analyze,basic,selcombo backbone protocoltb,SMD,2,lock 0 protocoltb,MD,2 Equilibration protocoltb,MD,3 MD scheme {VMD Classic} membrane,multi 1 protocoltb,SMD,2,restrsel {} protocoltb,MD,0,smd 0 protocoltb,MD,0,restrsel {} protocoltb,MD,2,smd 0 mdff,min 200 protocoltb,MD,0,restrIndex {} currenttime,0 {} analyze,advance,calcombo {H Bonds} currenttime,1 {} protocoltb,SMD,3,restrsel {} protocoltb,MD,1,lock 0 live 1 analyze,advance,hbondsel2entry {Type Selection} temperature,0 27 plength 200 protocoltb,SMD,3,saveAsTemplate 0 protocoltb,MD,1,restrsel {} solvent,boxbuffer 15 temperature,1 27 protocoltb,SMD,0 Minimization membrane,lipid POPC protocoltb,SMD,1 Annealing protocoltb,SMD,2 Equilibration analyze,basic,alientry {Type Selection} mdPrec,0 0 protocoltb,SMD,3 SMD protocoltb,MD,3,saveAsTemplate 0 protocoltb,MD,3,restrIndex {} pspeed 20 protocoltb,SMD,2,saveAsTemplate 0 protocoltb,SMD,2,restrIndex {} protocoltb,SMD,1,lock 0 protocoltb,MD,2,restrsel {} mdtime,0 10.0 analyze,basic,alicombo backbone mdtime,1 10.0 protocoltb,SMD,1,smd 0 protocoltb,MD,2,saveAsTemplate 0 membrane,ysize 30 protocoltb,SMD,3,smd 0 membrane,axis x protocoltb,SMD,1,saveAsTemplate 0 protocoltb,MD,3,lock 0 desktop {} saltconc,0 0.15 protocoltb,MD,3,restrsel {} protocoltb,MD,1,saveAsTemplate 0 protocoltb,MD,1,restrIndex {} protocoltb,MD,0,lock 0 protocoltb,SMD,0,saveAsTemplate 0 protocoltb,SMD,0,restrIndex {} analyze,advance,hbondsel1entry {Type Selection} saltions,0 NaCl protocoltb,MD,1,smd 0 analyze,basic,alicheck 0 protocoltb,SMD,3,lock 0 protocoltb,MD,3,smd 0 protocoltb,MD,0,saveAsTemplate 0 render,rendertype {Capture Display} solvent,0 Explicit solvent,minimalbox 0 protocoltb,SMD,0,lock 0 currenttime {Completed 0.000 of 0.000 ns} protocoltb,SMD,3,restrIndex {} protocoltb,SMD,0,restrsel {} protocoltb,MD,2,lock 0 protocoltb,SMD,0,smd 0 analyze,basic,selentry {Type Selection} protocoltb,SMD,1,restrsel {} membrane,xsize 30 protocoltb,SMD,2,smd 0 mdff,mdff 50000 protocoltb,MD,2,restrIndex {} } array set QWIKMD::chains {0,0 1 0,1 {B and protein} 0,2 {1 - 10}} array set QWIKMD::index_cmb {{B and protein,2} {0 blue} {B and protein,3} 0 {B and protein,4} rep1 {B and protein,1} NewCartoon {B and protein,5} {chain "B" and qwikmd_protein} } set QWIKMD::delete {} array set QWIKMD::mutate {} array set QWIKMD::protonate { } set QWIKMD::mutindex {} set QWIKMD::protindex {} set QWIKMD::renameindex {} array set QWIKMD::dorename {} set QWIKMD::patchestr {} set QWIKMD::state 0 set QWIKMD::load 1 set QWIKMD::prevconfFile {qwikmd_production_smd_0} set QWIKMD::confFile $QWIKMD::prevconfFile set QWIKMD::smd 1 set QWIKMD::anchorRes {10_B} set QWIKMD::anchorRessel {resid "10" and chain "B"} set QWIKMD::pullingRes {1_B} set QWIKMD::pullingRessel {resid "1" and chain "B"} QWIKMD::checkAnchors set QWIKMD::basicGui(live) 0 set QWIKMD::dcdfreq 100000 set QWIKMD::smdfreq 40 set QWIKMD::maxSteps {10000000}