############################################################# ## JOB DESCRIPTION ## ############################################################# # Simulate the 4-nanotube system with induced pressure difference ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure cnt_mod3.psf coordinates cnt.pdb set temperature 300 set outputname cnt_mod3 # Continuing a job from the restart files Bincoordinates initial.coor Binvelocities initial.vel ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_all27_prot_lipid.prm # Periodic Boundary conditions cellBasisVector1 23 0. 0. cellBasisVector2 0. 19.919 0. cellBasisVector3 0. 0 30.3962 wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 14.5 # Integrator Parameters timestep 1 ;# 1fs/step nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 # 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 # Output outputName $outputname restartfreq 1000 ;# 1000steps = every 1ps dcdfreq 1000 outputEnergies 100 # Fixed Atoms Constraint (set PDB occupancy-column to 1) fixedAtoms on # IMD Settings (can view sim in VMD) if {0} { IMDon on IMDport 3000 ;# port number (enter it in VMD) IMDfreq 1 ;# send every 1 frame IMDwait no ;# wait for VMD to connect before running? } ############################################################# ## EXTRA PARAMETERS ## ############################################################# tclForces on tclForcesScript { set LowerBoundary -12.5 set UpperBoundary 12.5 set force {0 0 0.4} set watIdList {} for {set i 577} {$i<1320} {incr i 3} { lappend watIdList $i addatom $i } proc calcforces {} { global watIdList LowerBoundary UpperBoundary force loadcoords coorList foreach i $watIdList { set z [lindex $coorList($i) 2] if {$z>$UpperBoundary || $z<$LowerBoundary} { addforce $i $force } } } } ############################################################# ## EXECUTION SCRIPT ## ############################################################# run 50000 ;# 100 ps