Preliminary NAMD/APBS Documantation

Last modified: 08/04/06 23:27:38 (rok)

NAMD/APBS Keywords

for details see GlobalMasterAPBS.C

Required keywords

keyword explanation
cglen Coarse grid side lengths
fglen Fine grid side lengths

Optional keywords

keyword explanation default (if any)
calc_type Calculation type 1
debug APBS Debugging level 0
nonlin Use NLPB? FALSE
bcfl Boundary condition method 1
srfm Surface calculation method 2
pdie Solute dielectric 2.0
sdie Solvent dielectric 78.4
sdens Vacc sphere density 10.0
srad Solvent radius 1.4
swin Cubic spline window 0.3
temp Temperature (in K) 298.15
gamma Surface tension for apolar energies/forces (in kJ/mol/A^2) 0.105
chgm Charge discretization method: 0: spl0; 1: spl2 1
calcenergy Energy calculation flag: 0: Do not perform energy calculation; 1: Calculate total energy only; 2: Calculate per-atom energy components 1
calcforce Atomic forces calculation: 0: Do not perform force calculation; 1: Calculate total force only; 2: Calculate per-atom force components 2
wpot Write electrostatic potential to iapbs-pot.dx FALSE
wchg Write charge data to iapbs-charge.dx FALSE
wsmol Write molecular surface ddata to iapbs-smol.dx FALSE
ion Counterion charge [e] and radius [A]
dime Grid dimensions (in x, y and z)
cmeth Centering method: 0: Center on a point 1: Center on a molecule 1
center Grid center if cmeth=0
ccmeth Coarse grid centering method: 0: Center on a point 1: Center on a molecule 1
ccenter Coarse grid center if ccmeth=0
fcmeth Fine grid centering method: 0: Center on a point 1: Center on a molecule 1
fcenter Fine grid center if fcmeth=0
grid Grid spacings
glen Grid side lengths
pdime Grid of processors to be used in calculation
ofrac Overlap fraction between processors 0.1
sp_apbs Perform single point energy calculation FALSE

Example

This is an example of NAMD input file which turns on APBS calculated solvation forces and energies: 

  
  amber on
  parmfile dipeptide.top
  ambercoor dipeptide.crd
  
  temperature 300
  
  exclude scaled1-4
  1-4scaling 0.8333333
  
  #timestep 2.0
  #rigidBonds all
  #fullElectFrequency 2
  
  
  switching on
  switchDist 9
  cutoff  10
  pairListDist 11
  
  outputname output
  outputEnergies 1
  outputTiming   100
  dcdFreq        500
  restartFreq    500
  wrapWater     on
  wrapNearest   on
  
  
  langevin          on
  langevinDamping   2
  langevinHydrogen  no
  langevinTemp     300
  
  
  apbsForces       on
  apbsPQRFile      dipeptide.pqr
  apbsForcesConfig {
    dime 33 33 33
    cglen    17.0071 13.8706 12.3012
    fglen    17.0071 13.8706 12.3012
    srfm 2
    chgm 1
    bcfl 1
    debug 0
    pdie 2.0000
    sdie 78.5400
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    gamma 0.105
    sp_apbs off
    wpot off
  }
  
  run 0