[gmx-users] g_rdf between bonded and nonbonded groups

[Emily Curtis]

I would like to calculate the inter- and intra-molecular radial distribution
functions separately.  I have read through g_rdf -h many times and I have a
few questions:

1.  I think that I may have to modify a trp file (and not use it for the
simulations) by setting the nrexcl to the number of bonds I would like the
calculation to exclude.  I cannot figure out where in the tpr file I should
add the nrexcl term.  I have tried to sort through the manual to figure out
how to make this modification but I cannot figure it out.  Does anyone have
any suggestions?

2.  In D.56 g_rdf of the Gromacs manual it says that the option -surf can be
used along with -rdf to only calculate the rdf of a molecule with its
closest neighbor in a set.  Can this option be used for calculating the
intramolecular radial distribution function or am I completely
misinterpreting the manual?  If it can be used how is this done?  I tried to
use it but I get the error message:  Invalid command line argument:
-surf

Thank you in advance for any help.

Emily
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