Butxt############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # apoCaM+7 in vacuo ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../ConfigurationTrials/apocam7.psf coordinates ../ConfigurationTrials/apocam7.pdb set temperature 300 set outputname ../ConfigurationTrials/apocam_7_eq firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../ConfigurationTrials/par_all22_prot_cmap.inp temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control #langevin on ;# do langevin dynamics #langevinDamping 5 ;# damping coefficient (gamma) of 5/ps #langevinTemp $temperature #langevinHydrogen off ;# don't couple langevin bath to hydrogens # Output outputName $outputname restartfreq 500 ;# 500steps = every 1ps dcdfreq 250 outputEnergies 100 outputPressure 100 ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 100 reinitvels $temperature run 2500 ;# 5ps runs:UCTxddGeneva UCgaqqGeneva  UCTxdd Lucida Grande UCgaxx Lucida Grande UCTxddGeneva UCgaqqGeneva  UCTxdd Lucida Grande UCgaxx Lucida Grande -UCTxddGeneva UCgaqqGeneva UCTxdd Lucida Grande UCgaxx Lucida Grande UCTxddGeneva UCgaqqGeneva UCTxdd Lucida Grande UCgaxx Lucida Grande UCTxzdd Lucida Grande UCgaTT Lucida Grande JUCTxddGeneva UCgaqqGeneva rlrs(brlrrext