############################################################# ## JOB DESCRIPTION ## ############################################################# # Simulated Annealing ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# ambercoor ../Minimise/filename.crd set temperature 0 set outputname filename_SAdyn set inputname filename_min binCoordinates $inputname.restart.coor extendedSystem $inputname.restart.xsc ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input amber yes parmfile filename.parm7 temperature $temperature # Force-Field Parameters readexclusions yes exclude scaled1-4 scnb 2.0 1-4scaling 0.833333 cutoff 999.0 switching off # 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 3 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature # Generalized Born Implicit Solvent (GBIS) parameters GBIS on ionConcentration 0.0 #distilled water alphaCutoff 25.0 #Onufriev, Bashford, Case (OBC_II): GBISDelta 1.00 GBISBeta 0.80 GBISGamma 4.85 # Restraint between monomers colvars on colvarsConfig restrain_monomers.conf colvarsInput $inputname.restart.colvars.state # Output outputName $outputname #restartfreq 2500 ;# 2500steps = every 5ps dcdfreq 100 outputEnergies 100 outputPressure 1000 ############################################################# ## EXECUTION SCRIPT ## ############################################################# set numcycles 10 set tempMax 800 set tempMin 0 set freq 10 set deltaT 50 set dynsteps 1000 set minsteps 500 set heatSteps [ expr $freq * (($tempMax - $tempMin) * 1 / $deltaT + 1 )] set coolSteps [ expr $freq * (($tempMax -50 - $tempMin) * 1 / $deltaT + 1 )] set minCoorSteps [ expr $heatSteps + $dynsteps + $coolSteps + $minsteps + 1] for {set i 1} {$i <= $numcycles} {incr i} { firsttimestep 0 for { set TEMP $tempMin } { $TEMP <= $tempMax } { incr TEMP $deltaT } { reinitvels $TEMP langevinTemp $TEMP run $freq } run $dynsteps for { set TEMP [ expr $tempMax - 50 ] } { $TEMP >= $tempMin } { incr TEMP -$deltaT } { reinitvels $TEMP langevinTemp $TEMP run $freq } minimize $minsteps outputName min_$i restartfreq $minCoorSteps }