# Continuing a job from the restart files if {1} { set inputname dec_heat binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem $inputname.xsc }
# Periodic Boundary conditions # NOTE: Do not set the periodic cell basis if you have also # specified an .xsc restart file! if {0} { cellBasisVector1 52. 0. 0. cellBasisVector2 0. 47. 0. cellBasisVector3 0. 0 49. cellOrigin 3.5 -0.5 -1.9 } wrapWater on wrapAll on
# Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume) if {0} { useGroupPressure yes ;# needed for 2fs steps useFlexibleCell no ;# no for water box, yes for membrane useConstantArea no ;# no for water box, yes for membrane
langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp $temperature }
# Fixed Atoms Constraint (set PDB beta-column to 1) if {0} { fixedAtoms on fixedAtomsFile dec-2238_wi.pdb fixedAtomsCol B }
# Harmonic restraint parameters if {0} { constraints on consexp 2 consref cfd_wi.cstr conskfile cfd_wi.cstr conskcol B }
# IMD Settings (can view sim in VMD) if {0} { IMDon on IMDport 3000 ;# port number (enter it in VMD) IMDfreq 1 ;# send every 1 frame IMDwait no ;# wait for VMD to connect before running? }