Assuming that your system comprises only protein, TIP3 waters, sodium and chloride ions, proceed as follows: Make /usr/local/toppar/non_charmm your working directory. Locate the files named top_opls_aa.inp and par_opls_aa_modified.inp. These are the topology and parameters files that you will have to use for your simulation (the parameter file has been modified to include parameters for the sodium and chloride ions, which explains the modified suffix).

Use the standard procedures to prepare, equilibrate and perform the production run of your simulation, substituting the above mentioned topology and parameters files as required. The only additional difference is that in the NAMD scripts you must add a line reading vdwGeometricSigma yes. The following excerpt from a NAMD script file should clarify matters:

#
# Input files
#
structure               ionized.psf
coordinates             ionized.pdb
vdwGeometricSigma       yes
parameters              par_opls_aa_modified.inp
paraTypeCharmm          on


#
# Output files & writing frequency for DCD
# and restart files
#
outputname              output/heat_out
binaryoutput            off
restartname             output/restart
restartfreq             1000
binaryrestart           yes
dcdFile                 output/heat_out.dcd
dcdFreq                 200