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 } amber on parmfile system.parm ambercoor system.crd bincoordinates win11_262.coor extendedSystem eq.xsc set outputname md.1 outputName $outputname firsttimestep 0 wrapWater on wrapAll on set temperature 310 temperature $temperature exclude scaled1-4 1-4scaling 0.83333 switching off cutoff 10. timestep 2.0 ;# 2fs/step (only if needed to finish quickly) rigidBonds all fullElectFrequency 2 stepspercycle 10 PME yes PMEGridSpacing 1.0 langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens useGroupPressure yes useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 50. langevinPistonTemp $temperature restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 5000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 colvars on colvarsConfig colvars.tcl run 75000