################################################### ## Job Description ################################################### # equilibrate popc lipid bilayer #################################################### ## Adjustable parameters #################################################### structure popc.psf coordinates popc.pdb set inputname bilayer_ratio_10_01.restart bincoordinates $inputname.coor binvelocities $inputname.vel extendedSystem $inputname.xsc outputname bilayer_ratio_10_02 set temperature 310 ################################################### ## Simulation parameters ################################################### firsttimestep 0 wrapWater on wrapAll on wrapNearest off paraTypeCharmm on parameters par_all36_lipid.prm exclude scaled1-4 1-4scaling 1.0 switching on switchdist 10 cutoff 12 pairlistdist 13.5 #margin 0 #constraints on #consexp 2 #consref tails_moving.pdb #conskfile tails_moving.pdb #conskcol B #cellbasisvector1 65.95 0 0 #cellbasisvector2 0 66.43 0 #cellbasisvector3 0 0 115.77 #cellorigin -13.67 -12.39 0.41 PME yes PMEgridspacing 1.0 rigidBonds all rigidTolerance 0.00000001 rigidIterations 100 useSettle on langevin on langevinTemp $temperature langevinDamping 5 langevinHydrogen no #temperature $temperature if {0} { useGroupPressure no ;#need for 2fs steps useFlexibleCell yes UseConstantArea yes ;# to keep the membrane area constant langevinPiston on LangevinPistonTarget 1 LangevinPistonPeriod 200 LangevinPistonDecay 100 LangevinPistonTemp $temperature } outputTiming 1000 outputEnergies 100 outputPressure 100 binaryoutput yes DCDfreq 1000 DCDUnitCell yes restartfreq 1000 restartsave no binaryrestart yes timestep 1.0 nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 ############################################### ## Extra parameters ############################################### #tclbc if {1} { set tclBCScript ../concGrad.tcl # only for TCBG local cluster if {1 } { foreach n [exec bpstat -n allup] { exec bpcp $tclBCScript $n:/tmp/ } exec cp $tclBCScript /tmp/ } tclBC on tclBCScript { # SOD for {set i 47834} {$i < 47856} {incr i} { lappend list1 $i } lappend allSerialLists $list1 lappend allRatios 10.0 # POT for {set i 47900} {$i < 47922} {incr i} { lappend list2 $i } lappend allSerialLists $list2 lappend allRatios 0.1 # set tclBCScript ../concGrad.tcl set tclBCScript /tmp/concGrad.tcl source $tclBCScript } set BOLTZMANN 0.0019872041 ;# kcal/mol*K set kT [expr $BOLTZMANN*$temperature] tclBCargs "$kT 10.0" } ##tclforces on ##tclforcesscript constraints_final_bilayer1.tcl ############################################### ## Execution script ############################################### #minimize 1000 run 5000000