Hello:
My student and I are currently trying to use Gromacs 4.0.5 to perform
some electrostatic analysis of nanostructures. One of our goals is to
implement the method of Dieter Wolf et al. (D. Wolf, P. Keblinski,
S.R. Phillpot and J. Eggebrecht, Journal of Chemical Physics 1999;
110:8254-8282) to calculate the Coulombic energy for ionic systems,
such that the periodicity assumptions inherent in the Ewald-type
approaches can be avoided.
In older versions of Gromacs, it appeared that there was a
shiftLR_correction implemented as one option to calculate the
Coulombic energies. However, in 4.0.5, we have found code in
ewald_util.c and ewald.c which should correspond to that for
shiftLR_correction, but we find that these functions are not actually
called when using the shiftLR_correction option. Modifying the
shiftLR_correction option is the best for us since the functional
forms of the Coulomb energy in the Wolf method is quite similar to
these.
Thus, I was wondering:
(1) Is the shiftLR_correction option obsolete in Gromacs 4.0.5?
(2) If so, what would be the best way to implement a new Coulombic
energy and force calculation approach (i.e. that of Wolf et al.) into
Gromacs?
Harold Park
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