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Title:NAMD Tutorial #1 - Simulation of a Simple Protein
Duration:16:41
Viewed:0
Published:04-05-2020
Source:Youtube

Thanks for watching! Contact me if you have any questions. If you don't want to download TCL or the maxmin script, or simply want to run a quicker simulation without periodic boundary conditions: 1) Remove everything in between the equals sign borders (PME, Grouppressure, Langevinpiston) 2) Remove "CellBasisVector" 1, 2 and 3, remove "CellOrigin" 3) Change "WrapWater" and "WrapAll" to off Download NAMD: www.ks.uiuc.edu/Development/Download/download.cgi?… CHARMM topologies and parameters: mackerell.umaryland.edu/charmm_ff.shtml Maxmin script: m3g.iqm.unicamp.br/packmol/utilities.shtml MAXMIN_NEW ADDITIONS: puts " Cell centre: " puts " X= [ expr ($xmax + $xmin)/2 ] " puts " Y= [ expr ($ymax + $ymin)/2 ] " puts " Z= [ expr ($zmax + $zmin)/2 ] " puts "-------------------------------------------------------" puts " Copy/paste for NAMD: " puts "cellBasisVector1 [ expr $xmax - $xmin ] 0 0 " puts "cellBasisVector2 0 [ expr $ymax - $ymin ] 0 " puts "cellBasisVector3 0 0 [ expr $zmax - $zmin ] " puts "cellOrigin [ expr ($xmax + $xmin)/2 ] [ expr ($ymax + $ymin)/2 ] [ expr ($zmax + $zmin)/2 ] " puts "-------------------------------------------------------" NAMD INPUT SCRIPT THAT I USED: # ----------input----- coordinates solvate.pdb structure solvate.psf parameters param.prm paratypecharmm on #bincoordinates minimized.restart.coor #binvelocities minimized.restart.vel # ----------output------ set output output outputname $output dcdfile ${output}.dcd xstFile ${output}.xst dcdfreq 50 xstFreq 50 binaryoutput yes binaryrestart yes outputEnergies 50 restartfreq 50 # ---------Basic dynamics------- exclude scaled1-4 1-4scaling 1 COMmotion no dielectric 1.0 # --------Simulation space partitioning---- switching on switchdist 9 cutoff 10 pairlistdist 11 # --------Multiple time stepping---- firsttimestep 0 timestep 2 stepspercycle 1 # -------Temperature control---- set temperature 310 temperature $temperature; # initial temperature # -------Langevin Dynamics------ langevin on; # do langevin dynamics langevinDamping 1; # damping coefficient (gamma) of 1/ps langevinTemp $temperature; # bath temperature # =============================================== PME on PMEGridSizeX 65 PMEGridSizeY 50 PMEGridSizeZ 55 # doesnt work with just pme useGroupPressure yes # with grouppressure, works better, holes still there LangevinPiston on LangevinPistonTarget 1.02 LangevinPistonPeriod 150 LangevinPistonDecay 90 LangevinPistonTemp $temperature # with langevin piston, works!!! But slower. # =============================================== # Periodic Boundary conditions cellBasisVector1 64.702 0 0 cellBasisVector2 0 49.82 0 cellBasisVector3 0 0 55.158 cellOrigin -5.7379999999999995 22.462999999999997 20.051000000000002 wrapWater on ;# wrap water to central cell wrapAll on ;# wrap other molecules too wrapNearest off # ---------Scripting minimize 100 ;# lower potential energy for 1000 steps reinitvels $temperature ;# since minimization zeros velocities run 50000; # END

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