From: Mo Chen (mochen.mmm_at_gmail.com)
Date: Fri May 30 2014 - 19:35:50 CDT
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.
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