From: Thomas C. Bishop (
Date: Tue Jun 15 2010 - 17:34:27 CDT

Dear Dr. NAMD,

I am using the pairinteraction options to calculate pair interaction energies
in my simulations.

If I turn this option on during "production runs" does this change the
dynamics in any way or does it just change the reporting of energies in the
output file? (it's not entirely clear from the manual)

As a followup If I have a solvated ligand-receptor system is there a way
during production runs to obtain all of the following w/out having to
"recompute" values from a dcd:

1) ligand self energy
2) receptor self energy
3) interaction energy between ligand and receptor?

Pointers to any scripts in addtion to ones in the manual/script library would
be much appreciated.


   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392

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