AMBER Archive (2007)

Subject: AMBER: GB Energy Spreads for MD Structures

From: adelene_at_Stanford.EDU
Date: Mon May 07 2007 - 14:19:47 CDT

This question is more specific to NAB and APBS, but I'm trying my luck here.

I'm working on calculating the solvation energies of structures
obtained from MD simulations by NAB and entering them into APBS for
calculation.

This might seem to be a silly question, but I'm perturbed as to why
there is a huge energy spread in the energies I obtain from APBS, much
like those in figure 1 of this paper (Tsui V., Case D.A., "Molecular
Dynamics Simulations of Nucleic Acids with a Generalized Born
Solvation Model", J. Am. Chem. Soc., 2000, 122, 2489). For a
particular RNA/DNA, MD appears to generate snapshots with
electrostatic energies (calculated using GB or Poisson Boltzmann) with
variation of several hundred kT (~300-500). Is there another
contribution to the total energy that is balancing out the
fluctuations in electrostatic energy?

Thanks!

Adelene

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