############################################################################################ # NAMD ABF setup for free enrgy profile of UO2.2NO3 at water and Hexane interface # ############################################################################################ #Simulation with 874 water molecules and 143 hexane molecules # Constant temperature # system originally built in charmm ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# #molecules structure nam-equil.psf #zero_w_namd.psf ;#src/solv3_counter_box_namd.psf coordinates nam-equil.pdb #pmf_out/mini.output.coor ;#zero_w_namd.pdb ;#src/solv3_counter_box_namd.pdb outputName pmf_out/abf.output firsttimestep 0 set temperature 300 #bincoordinates pmf_out/1ots_namd.1.restart.1000.coor #binvelocities pmf_out/1ots_namd.1.restart.1000.vel #extended system pmf_out/1ots_namd.1.restart.1000.xsc ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters tbp.prm temperature $temperature # periodic cell cellBasisVector1 30.00 0 0 cellBasisVector2 0 30.00 0 cellBasisVector3 0 0 100.00 wrapAll on wrapNearest on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 8.0 pairlistdist 13.0 margin 1 ;#3 # full electrostatics PME on PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 128 # Integrator Parameters timestep 1.0 ;# 1fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 binaryoutput no dcdfreq 100 ;# 500steps = every 1ps outputEnergies 100 #outputPressure 100 restartname pmf_out/md.restart restartsave yes restartfreq 500 XSTfile 1ots_namd_1 XSTfreq 500 #outputname 1ots_namd_1.1 ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Tcl interface #tclForces on #tclForcesScript 1ots.tcl ;#clc0_3_2m7_npt.tcl #fixedAtoms on #fixedAtomsFile src/solv3_counter_box_namd_fixed.pdb #fixedAtomsCol X #fixedAtoms on ##fixedAtomsFile src/solv3_counter_box_namd_fixpol_b1.pdb ;#src/solv3_box_namd_fixpol1.pdb #fixedAtomsFile src/solv3_counter_box_namd_fixpol1.pdb #fixedAtomsCol B #run 10000 ## ABF source /usr/local/NAMD_2.6b1_Source/lib/abf/abf.tcl #abf restraintList { # dihe1 {dihe {ETH,1,HI1} {ETH,1,CI} {ETH,1,CM} {ETH,1,HM1} 20.0 0.0} #} abf coordinate zCoord abf abf2 { 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 } set water 2872 for {set n 1} {$n < 874} {incr n} {append water " [expr {2872 + $n * 3} ]"} abf abf1 $water abf ximin 4 abf ximax 8 abf dxi 0.04 abf forceConst 0.02 abf applyBias no #abf dsmooth 1.0 abf fullsamples 20 abf outfile pmf_out/zero.abf abf historyfile pmf_out/zero_abf.his abf outputfreq 5 abf writexifreq 10 abf distfile pmf_out/zero_abf.dis #abf value zCoord # Execution Script run 50000