AMBER Archive (2007)

Subject: Re: AMBER: GB Energy Spreads for MD Structures

From: David A. Case (case_at_scripps.edu)
Date: Mon May 07 2007 - 16:13:41 CDT

On Mon, May 07, 2007, adelene_at_stanford.edu wrote:
>
> 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).

This doesn't directly address your question, but might be a useful starting
point:

    http://amber.ch.ic.ac.uk/archive/200608/0329.html

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu