NAMD

• • www.ks.uiuc.edu/Research/namd.

• Membrane Builder.

A sample of NAMD input script

structure ../step5_assembly.xplor_ext.psf

coordinates ../step5_assembly.pdb

set temp 310;

outputName step7.1_production-res3; # base name for output from this run

# NAMD writes two files at the end, final coord and vel

# in the format of first-dyn.coor and first-dyn.vel

set inputname step7.1_production-res2.restart;

binCoordinates $inputname.coor; # coordinates from last run (binary)

binVelocities $inputname.vel; # velocities from last run (binary)

extendedSystem $inputname.xsc; # cell dimensions from last run (binary)

restartfreq 5000; # 500 steps = every 1ps

dcdfreq 5000;

dcdUnitCell yes; # the file will contain unit cell info in the style of

firsttimestep 4780000; # charmm dcd files. if yes, the dcd files will contain

# unit cell information in the style of charmm DCD files.

xstFreq 5000; # XSTFreq: control how often the extended systen configuration

# will be appended to the XST file

outputEnergies 5000; # 125 steps = every 0.25ps

# The number of timesteps between each energy output of NAMD

outputTiming 5000; # The number of timesteps between each timing output shows

# time per step and time to completion

# Force-Field Parameters

paraTypeCharmm on; # We're using charmm type parameter file(s)

# multiple definitions may be used but only one file per definition

parameters toppar/par_all36_prot.prm;

parameters toppar/par_all36_na.prm;

parameters toppar/par_all36_carb.prm;

parameters toppar/par_all36_lipid.prm;

parameters toppar/par_all36_cgenff.prm;

parameters toppar/toppar_water_ions.str;

parameters toppar/toppar_all36_lipid_cholesterol.str;

# extra lipids

parameters toppar/toppar_all36_carb_glycolipid.str;

parameters toppar/toppar_all36_lipid_bacterial.str;

parameters toppar/toppar_all36_lipid_sphingo.str;

parameters toppar/toppar_all36_carb_glycopeptide.str;

parameters toppar/toppar_all36_prot_fluoro_alkanes.str;

parameters toppar/toppar_all36_prot_na_combined.str;

parameters toppar/toppar_all36_lipid_miscellaneous.str;

parameters toppar/toppar_all36_lipid_yeast.str;

parameters toppar/toppar_dum_noble_gases.str;

parameters toppar/toppar_all36_na_nad_ppi.str;

parameters toppar/toppar_all36_lipid_inositol.str;

parameters toppar/toppar_all36_lipid_cardiolipin.str;

parameters toppar/toppar_all36_carb_glycopeptide.str;

# These are specified by CHARMM

exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"

# 1-2: all atoms pairs that are bonded are going to be ignored

# 1-3: 3 consecutively bonded are excluded

# scaled1-4: include all the 1-3, and modified 1-4 interactions

# electrostatic scaled by 1-4scaling factor 1.0

# vdW special 1-4 parameters in charmm parameter file.

1-4scaling 1.0

switching on

vdwForceSwitching yes; # New option for force-based switching of vdW

# if both switching and vdwForceSwitching are on CHARMM force

# switching is used for vdW forces.

# You have some freedom choosing the cutoff

cutoff 9.0; # may use smaller, maybe 10., with PME

switchdist 7.0; # cutoff - 2.

# switchdist - where you start to switch

# cutoff - where you stop accounting for nonbond interactions.

# correspondence in charmm:

# (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)

pairlistdist 11.0; # stores the all the pairs with in the distance it should be larger

# than cutoff( + 2.)

stepspercycle 20; # 20 redo pairlists every ten steps

pairlistsPerCycle 2; # 2 is the default

# cycle represents the number of steps between atom reassignments

# this means every 20/2=10 steps the pairlist will be updated

# Integrator Parameters

timestep 2.0; # fs/step

rigidBonds all; # Bound constraint all bonds involving H are fixed in length

nonbondedFreq 1; # nonbonded forces every step

fullElectFrequency 1; # PME every step

wrapWater on; # wrap water to central cell

wrapAll on; # wrap other molecules too

wrapNearest off; # use for non-rectangular cells (wrap to the nearest image)

# PME (for full-system periodic electrostatics)

source checkfft.str

PME yes;

PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)

PMEGridSizeX $fftx; # should be close to the cell size

PMEGridSizeY $ffty; # corresponds to the charmm input fftx/y/z

PMEGridSizeZ $fftz;

# Constant Pressure Control (variable volume)

useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and

# has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)

useFlexibleCell yes; # yes for anisotropic system like membrane

useConstantRatio yes; # keeps the ratio of the unit cell in the x-y plane constant A=B

langevinPiston on; # Nose-Hoover Langevin piston pressure control

langevinPistonTarget 1.0; # target pressure in bar 1atm = 1.01325bar

langevinPistonPeriod 50.0; # oscillation period in fs. correspond to pgamma T=50fs=0.05ps

# f=1/T=20.0(pgamma)

langevinPistonDecay 25.0; # oscillation decay time. smaller value correspons to larger random

# forces and increased coupling to the Langevin temp bath.

# Equall or smaller than piston period

langevinPistonTemp $temp; # coupled to heat bath

# Constant Temperature Control

langevin on; # langevin dynamics

langevinDamping 1.0; # damping coefficient of 1/ps (keep low)

langevinTemp $temp; # random noise at this level

langevinHydrogen off; # don't couple bath to hydrogens

# run

numsteps 500000000; # run stops when this step is reached

run 50000000; # 1ns