From: Christopher Von Bargen (cdvonbargen_at_gmail.com)
Date: Thu Nov 07 2013 - 15:22:58 CST
A question concerning pairInteractionSelf:
When using tools like this (ie with the NAMD Energy plugin for VMD), it
would be helpful to make it clear what terms are being included in the
calculation of the potential.
For instance, If I load a united atom propane molecule (3 connected carbon
atoms, with 2 bonds and 1 angle), I would expect flagging only the first
two connected carbon atoms in the pdb provided to pairInteractionFile would
only output the energy of the bond between the two. In fact, using
pairInteractionSelf on that selection outputs the sum of both bond
potentials and the angle potential for the system. I suspect that what the
flagging in the pairInteractionFile pdb is doing is including any bonding
terms that include atoms that have been flagged; as opposed to calculating
energies for terms that *only* include atoms that have been flagged.
Am I interpreting this behavior correctly? If so, is there somewhere else
in the manual that indicates this? The current discussion of
doesnt make any indication that this is the behavior I should expect.
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