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Pressure profile calculations

NAMD supports the calculation of lateral pressure profiles as a function of the z-coordinate in the system. The algorithm is based on that of Lindahl and Edholm (JCP 2000), with modifications to enable Ewald sums based on Sonne et al (JCP 122, 2005).

The simulation space is partitioned into slabs, and half the virial due to the interaction between two particles is assigned to each of the slabs containing the particles. This amounts to employing the Harasima contour, rather than the Irving-Kirkwood contour, as was done in NAMD 2.5. The diagonal components of the pressure tensor for each slab, averaged over all timesteps since the previous output, are recorded in the NAMD output file. The units of pressure are the same as in the regular NAMD pressure output; i.e., bar.

The total virial contains contributions from up to four components: kinetic energy, bonded interactions, nonbonded interactions, and an Ewald sum. All but the Ewald sums are computed online during a normal simulation run (this is a change from NAMD 2.5, when nonbonded contributions to the Ewald sum were always computed offline). If the simulations are performed using PME, the Ewald contribution should be estimated using a separate, offline calculation based on the saved trajectory files. The nonbonded contribution using a cutoff different from the one used in the simulation may also be computed offline in the same fashion as for Ewald, if desired.

Pressure profile calculations may be performed in either constant volume or constant pressure conditions. If constant pressure is enabled, the slabs thickness will be rescaled along with the unit cell; the dcdUnitCell option will also be switched on so that unit cell information is stored in the trajectory file.

NAMD 2.6 now reports the lateral pressure partitioned by interaction type. Three groups are reported: kinetic + rigid bond restraints (referred to as ``internal", bonded, and nonbonded. If Ewald pressure profile calculations are active, the Ewald contribution is reported in the nonbonded section, and no other contributions are reported.

NAMD 2.6 also permits the pressure profile to be partitioned by atom type. Up to 15 atom groups may be assigned, and individual contribution of each group (for the ``internal" pressures) and the pairwise contributions of interactions within and between groups (for the nonbonded and bonded pressures) are reported in the output file.

Here is an example snippet from a NAMD input that can be used to compute the Ewald component of the pressure profile. It assumes that the coordinates were saved in the dcd file pp03.dcd) every 500 timesteps.

Pme             on
PmeGridSizeX    64
PmeGridSizeY    64
PmeGridSizeZ    64

exclude         scaled1-4
1-4scaling      1.0  

switching on
switchdist      9
cutoff          10
pairlistdist    11

pressureProfile        on
pressureProfileSlabs   30
pressureProfileFreq    100
pressureProfileAtomTypes 6
pressureProfileAtomTypesFile atomtypes.pdb
pressureProfileEwald  on
pressureProfileEwaldX  16
pressureProfileEwaldY  16
pressureProfileEwaldZ  16

set ts 0
firstTimestep $ts

coorfile open dcd pp03.dcd
while { [coorfile read] != -1 } {
  incr ts 500
  firstTimestep $ts
  run 0
coorfile close

next up previous contents index
Next: Translation between NAMD and Up: Runtime Analysis Previous: Pair interaction calculations   Contents   Index