############################################################# ## JOB DESCRIPTION ## ############################################################# ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# genCompressedPsf on structure RanEctGag.psf #coordinates meltEct3C35.pdb bincoordinates meltEct.3C35.restart.coor set outputname testPSF4 set temperature 310 set runSteps 500 # restart file :input in either inputname or cellBasis # 0 is new run, 1 is restart run, 2 is restart run from old files. set restartfoo 0 set inputname testPSF proc get_first_ts { xscfile } { set fd [open $xscfile r] gets $fd gets $fd gets $fd line set ts [lindex $line 0] close $fd return $ts } if { $restartfoo == 0 } { temperature $temperature } elseif { $restartfoo == 1 } { bincoordinates ./$inputname.coor binvelocities ./$inputname.vel extendedSystem ./$inputname.xsc #set firsttime [get_first_ts ./$inputname.xsc] set firsttime 0; firsttimestep 0; } elseif { $restartfoo == 2 } { bincoordinates ./$inputname.restart.coor binvelocities ./$inputname.restart.vel extendedSystem ./$inputname.restart.xsc set firsttime [get_first_ts ./$inputname.restart.xsc] firsttimestep $firsttime } elseif { $restartfoo == 3 } { bincoordinates ./$inputname.restart.coor.old binvelocities ./$inputname.restart.vel.old extendedSystem ./$inputname.restart.xsc.old set firsttime [ get_first_ts ./$inputname.restart.xsc.old ] firsttimestep $firsttime } ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../99_common/par_all22_prot_cmap.inp; parameters ../99_common/par_all36_carbMOD3.prm; parameters ../99_common/toppar_all36_glycopeptideMOD3.str; parameters ../99_common/parGCCXsulf.inp # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! # temperature $temperature # Periodic Boundary conditions # NOTE: Do not set the periodic cell basis if you have also # specified an .xsc restart file! wrapWater off wrapAll off # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14 margin 3 # Integrator Parameters timestep 1.0 nonbondedFreq 1 fullElectFrequency 1 stepspercycle 20 if { 0 } { #GBIS parameters GBIS on ionConcentration 0.1 alphaCutoff 14 #nonbonded parameters switching on switchdist 15 cutoff 16 pairlistdist 17.5 #multistep parameters timestep 1 #nonbondedFreq 2 #fullElectFrequency 4 } #PME (for full-system periodic electrostatics) PME off # Constant Temperature Control if { 1 } { langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens } # Output outputName $outputname restartname $outputname.restart dcdfile $outputname.dcd #veldcdfile $outputname.veldcd xstFile $outputname.xst restartfreq 100 dcdfreq 100 xstFreq 100 outputEnergies 100 outputPressure 100 ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Put here any custom parameters that are specific to # this job (e.g., SMD, TclForces, etc...) ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization if { $restartfoo == 0 } { minimize 100 reinitvels $temperature #run 10000 run $runSteps } else { set stepP [expr $runSteps - $firsttime ] run $stepP ; }