Using NAMD to calculate pair energy with many subset permutations

From: brmorgan_at_clarku.edu
Date: Wed Oct 15 2008 - 13:08:42 CDT

Hello,

I am using NAMD to calculate pair-interaction energies for various subsets
of atoms within a trajectory. The problem is that with 121 (and growing)
different permuations of coordinate files and subsets of atoms, running
each one with its own individual configuration file is very tedious and
error prone. I have tried running different combinations of
pairInteractionGroup numbers within the same configuration file, but it
seems impossible to change the pairInteractionGroup numbers after the
first 'run' statement.

Can anyone suggest an alternate approach? I have attached my trial
configuration file (based off the one automatically generated by VMD's
NAMDenergy) in case my explanation is unclear.

Thank you,
Brittany

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