NAMD2.7 settings  Note  Corresponding Amber11 settings 
Force Field Settings  
amber on  Use Amber FF, expect to read a PARM7 file.  default in amber 
switching off  Do not use switching  default in amber 
exclude scaled14  14 interactions are scaled by scnb and 14scaling, 13 interactions are ignored.  default in amber 
14scaling 0.833333333  Scaling factor for 14 electrostatic interaction(0.833333333=1.0/1.2).  scee=1.2 
scnb 2.0  14 vdW interactions are divided by scnb.  scnb=2.0 
readexclusions yes  Read exclusion lists from the PARM7 file.  default in amber 
cutoff 9  Cutoff for vdW and electrostatic interactions.  cut=9 
watermodel {tip3, tip4}  Expect water residues to be TIP3P or TIP4P type.  detected automatically 
pairListDist 11  Distance between pairs of atoms for inclusion in pair lists that are used to calculate vdW and electrostatic interactions.  skinnb=2.0 
LJcorrection on  Apply an analytical tail correction to the reported vdW energy and virial that is equal to the amount lost due to switching and cutoff of the LJ potential.  vdwmeth=1 
ZeroMomentum on  Remove center of mass drift due to PME.  netfrc = 1 
rigidBonds {water, all}  SHAKE bonds that contain H atoms from water residues or all residues.  ntc=2, ntf=2, noshakemask = ... 
rigidTolerance 1.0e8  SHAKE tolerance.  tol=1.0e8 
rigidIterations 100  SHAKE maximum iterations.  N/A 
useSettle {on}  Use faster SETTLE instead of SHAKE for bonds belonging to water molecules. Default option in namd is on.  jfastw=0 
timeStep 1.0  Integration time step in fs.  dt=0.001 
Nonbonded interactions  
fullElectFrequency 1  The number of timesteps between each full electrostatics evaluation.  N/A 
nonBondedFreq 1  How often shortrange nonbonded interactions should be calculated.  N/A 
stepspercycle 10  Number of timesteps in each cycle. Each cycle represents the number of timesteps between atom reassignments to pair lists.  nbflag=0, nsnb=10 (although here I let amber do its default behavior) 
PME on  Use PME.  always ON if ntb>0 
PMEGridSizeX intx, PMEGridSizeY inty, PMEGridSizeZ intz 
The size of the fftw grid on each dimention.  nfft1=intx , nfft2=inty, nfft3=intz 
PMETolerance 1.0e6  PME direct space tolerance.  dsum_tol=1.0e6 
PMEInterpOrder 4 (i.e. cubic spline)  PME interpolation order.  order=4 
cellBasisVector1 x1 y1 z1, cellBasisVector1 x2 y2 z2, cellBasisVector1 x3 y3 z3 
The periodic cell vectors.  Defined indirectly at the bottom of thr .rst/.crd files. 
cellOrigin x y z  Used as the center of the cell for wrapped output coordinates.  N/A 
Temperature Control  Thermostats [A] [A]
Note that PMEMD and NAMD provide more than the Langevin thermostat for pressure regulation. Sander and PMEMD provide the Andersen thermostat. NAMD implements the LoweAndersen thermostat. Please consult the users manuals for more details.


langevin {on,off}  Use Langevin thermostat.  ntt=3 
langevinDamping 5  Damping coefficient for Langevin dynamics in ps^{ − 1}.  gamma_ln = 5 
langevinTemp 300  Langevin thermostat target temperature in K.  temp0 = 300 
langevinHydrogen off  Turn off the Langevin thermostat coupling of hydrogens.  default in amber (?) 
temperature 300  If no initial velocities are provided, choose this as the inital temperature.  tempi = 300 
Pressure Control  Barrostats [B] [B]
Note that NAMD users usually chose to use NoséHoover Langevin barrostat instead of the Beredensen version.


BerendsenPressure {on,off}  Use Beredensen barrostat.  ntp=1 
BerendsenPressureTarget 1.01325  Target Pressure in bars.  pres0 = 1.01325 
BerendsenPressureRelaxationTime 100.0  Relaxation time for the Beredensen barrostat in ps for PMEMD and fs for NAMD.  taup = [1.0,5.0] 
useGroupPressure yes (needed for rigidBonds), useFlexibleCell no useConstantArea no 
Isotropic pressure scaling.  set when ntp=1 
Minimization, Dynamics  
minimize nsteps  Do minimization for nsteps.  imin=1, maxcyc = nsteps 
run nsteps  Run dynamics.  imin =0, nstlim = nsteps 
AMBER = 332.0522173 CHARMM = 332.054 NAMD = 332.0636
#define COULOMB 332.0522173
cellBasisVector1 d 0.0 0.0 cellBasisVector2 (1/3)*d (2/3)sqrt(2)*d 0.0 cellBasisVector3 (1/3)*d (1/3)sqrt(2)*d (1/3)sqrt(6)*d
d d d 109.4712190 109.4712190 109.4712190
cellBasisVector1 d 0.0 0.0 cellBasisVector2 (1/2)*d (1/2)sqrt(3)*d 0.0 cellBasisVector3 (1/2)*d (1/6)sqrt(3)*d (1/3)sqrt(6)*d
cellBasisVector1 d 0.0 0.0 cellBasisVector2 0.0 d 0.0 cellBasisVector3 (1/2)*d (1/2)*d (1/2)sqrt(2)*d
d d d 60.0 60.0 60.0 or d d d 60.0 60.0 90.0
cellBasisVector1 d 0.0 0.0 cellBasisVector2 (1/2)*d (1/2)sqrt(3)*d 0.0 cellBasisVector3 0.0 0.0 h
d d h 60.0 90.0 90.0
source leaprc.ff10 WAT = T4E loadAmberParams frcmod.tip4pew set default FlexibleWater on x = loadpdb "SOURCE.pdb" saveamberparm x x.parm7 x.crd savepdb x x.pdb quit
Typical Production MD NVE &cntrl ntx=1, irest=0, ntc=2, ntf=2, tol=1.0e8, nstlim=1000, dt=0.001, ntpr=1, ntwx=1, ntwr=1, cut=9.0 ntt=0, ntb=1, ntp=0, ioutfm=1, ntave=1000 / &ewald dsum_tol = 1.0e6 nfft1=72, nfft2=72, nfft3=72, order=4, /
## OUTPUT/INPUT # Amber/(t,s,x)leap generated parm and crd file parmfile prmtop ambercoor xyz # Input bincoordinates input.restart.coor binvelocities input.restart.vel extendedSystem input.restart.xsc # Output restartfreq 1000 dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 outputname output temperature 0 ## SIMULATION PARAMETERS # AMBER FF settings amber on rigidBonds all useSettle on rigidTolerance 1.0e8 cutoff 9.0 pairlistdist 11.0 switching off exclude scaled14 readexclusions yes 14scaling 0.83333333 scnb 2.0 zeromomentum on ljcorrection on watermodel tip3 # Integrator Parameters timestep 1.00 nonbondedFreq 1 fullElectFrequency 1 stepspercycle 10 # Constant Temperature Control is off langevin off # Constant Pressure Control is off langevinPiston off # PME settings PME on PMETolerance 1.0e6 PMEInterpOrder 4 FFTWUseWisdom no PMEGridSizeX 54 PMEGridSizeY 54 PMEGridSizeZ 54 # periodic cell cellBasisVector1 50.8726134 0.0 0.0 cellBasisVector2 0.0 50.8903175 0.0 cellBasisVector3 0.0 0.0 50.8639184 cellOrigin 0.0 0.0 0.0 ## EXECUTION SCRIPT run 100000