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Minimal Examples

Constant-pH simulations can be carried out with largely the same options as conventional MD simulations (with some exceptions, see previous sections). The follwing examples assume that: 1) PSF and PDB files for the system of interest have already been constructed and 2) appropriate simulation keywords have already been chosen (e.g., for PME, Langevin dynamics, etc.).

# End conventional settings...
source .../namd/lib/namdcph/namdcph.tcl
# Constant-pH MD requires additional force field files _during_ the simulation.
# In general, all RTFs used to construct the system need to be included with
# the ``topology'' command (just as in psfgen). Additional constant-pH specific
# RTF and PRM files are also necessary, as well as an accompanying
# configuration file in JSON format.
#
cphConfigFile <path to JSON config file>
topology <path to RTF>
topology <path to another RTF>
pH 7.0
# The following defaults all nonequilibrium switches to 5000 steps and then
# increases the time for residue 5 of segid PROA to 7500 steps -- multiple
# residues can be specified 
#
cphNumStepsPerSwitch 5000 PROA:5:ASP 7500
# Run 100 minimization cycles before starting dynamics.
cphNumMinSteps 100
# Run 2500 steps of MD between attempted protonation state changes. Run 10
# cycles of MD and neMD/MC. The _upper_ bound of the simulation is thus:
#
# 10*(2500 + 7500) = 100000 steps
#
# but the actual simulation may be shorter in length.
#
cphRun 2500 10

Restarting a simulation

The following assumes that a simulation has already been run (as in the example above). For clarity we shall assume that outputname was set to "foo" such that restart files have been written to foo.coor and foo.vel (normal output) as well as foo.psf, foo.pdb, and foo.cphrst (constant-pH specific output).

# End conventional settings...
source .../namd/lib/namdcph/namdcph.tcl
# Constant-pH MD requires additional force field files _during_ the simulation.
# In general, all RTFs used to construct the system need to be included with
# the ``topology'' command (just as in psfgen). Additional constant-pH specific
# RTF and PRM files are also necessary, as well as an accompanying
# configuration file in JSON format.
#
cphConfigFile <path to JSON config file>
topology <path to RTF>
topology <path to another RTF>
pH 7.0

structure foo.psf
coordinates foo.pdb
binCoordinates foo.coor
binVelocities foo.vel
cphRestartFile foo.cphrst
# NB: switch times and inherent pKa values are read here and no longer need to
# be specified as during initialization

cphRun 2500 10



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