[gmx-users] (no subject)

gmx-users-admin at gromacs.org gmx-users-admin at gromacs.org
Tue Oct 29 08:12:03 CET 2002

Hello all,

I am interested in using David van der Spoel's method for calculating the
total coulomb energy of a single ion with the rest of the system.  I just
want to ask a few questions so I can feel comfortable with what I'm doing.

1)If I take the original .edr file from the simulation, is the total
coulomb energy of the system Coulomb (SR) + Coulomb (LR) as extracted by
g_energy?  That is.. Coulomb 1-4 doesn't really factor in does it?

2)Then if I set the ion charge to zero and rerun to generate a new .edr
file and calculate the total coulomb energy again as Coulomb (SR) + Coulomb
(LR), this will be the total PME energy for System_&_!ion-System_&_!ion?

3)Then I can subtract the result of #2 from the result of #1 and obtain the
total coulomb PME energy of System_&_!ion-ion?  Since there is only one
ion, the coulomb energy of ion-ion is zero so I don't have to worry about

4)If I write the total ewald sum in the traditional way,

      E = E(real) + E(reciprocal) + E(self) + E(dipole_correction)

  is the coulomb energy as extracted by g_energy as follows:

   Coulomb (SR) = E(real)


   Coulomb (LR) = E(reciprocal) + E(self) + E(dipole_correction) ?

   How exactly are these terms divided among the two quantities Coulomb(SR)
   and Coulomb(LR)?

Many Thanks in advance,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

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