From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Sat May 31 2014 - 12:01:34 CDT
NAMD and GROMACS should be calculating the same mathematical form for PME.
The paragraph you quote below from the NAMD User's Guide is imprecisely written. Particularly the last sentence. The long-range component consists of the smoothed electrostatic interactions between all particles, which then permits fast computation on a grid.
Your final question is vague. Significant deviations over long MD simulations might occur from "slightly different methods for short-range electrostatic energy," but would likely be more strongly influenced by the integration method.
On May 30, 2014, at 7:35 PM, Mo Chen <mochen.mmm_at_gmail.com> wrote:
> Dear NAMD developers,
> I have a question about how NAMD calculate electrostatic energy.
> As cited from NAMD Guide 7.3.4:
> "In this scheme, the total force acting on each atom is broken into two pieces, a quickly varying local component and a slower long range component. The local force component is
> defined in terms of a splitting function. The local force component consists of all bonded and van der Waals interactions as well as that portion of electrostatic interactions for pairs that are separated by less than the local interaction distance determined by the splitting function. The long range component consists only of electrostatic interactions outside of the local interaction distance."
> Does this mean that in NAMD when using PME, the electrostatic energy within cutoff is the coulomb potential and the electrostatic energy outside cutoff is the long-range term calculated by PME? If so, there seems to be a little difference in calculating the short-range term between NAMD and GROMACS. Below is the short-range potential in GROMACS.
> May I ask if using the two slightly different methods for short-range electrostatic energy would result in significant deviations over long MD simulations? Thank you very much.
> Best regards,
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/
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