[gmx-users] "Coul. Recip." in Logfile for Classical Ewald
mark.j.abraham at gmail.com
Wed Sep 3 22:17:09 CEST 2014
In the group cut-off scheme, Coul Recip also contains exclusions for (e.g.)
atoms in the central cell that share bonds, which are computed in
gmxlib/ewald_util.c. You would need to compare with a run without bonds, or
do some more printf.
On Wed, Sep 3, 2014 at 7:53 PM, Barnett, James W. <jbarnet4 at tulane.edu>
> I'm doing a classical Ewald simulation with GROMACS (obviously I should be
> using something other than Ewald in my simulations like PME, but I am just
> trying to understand the concept and write some analysis code.). In the
> logfile does "Coul. Recip." include the self correction (or any other kind
> of correction)? I'm having a little trouble seeing where the specific
> number comes from and am trying to understand. Adding up the kspace
> contribution (from GROMACS) and self contribution (my own calculation)
> doesn't seem to get me the number from the logfile. I know I'm missing
> As an example I ran 33 SPC waters in a 1 x 1 x 1 box with cutoffs at 0.4
> (this is just a small quick simulation to get some numbers for this
> purpose). Again this is classical Ewald, fourierspacing is the default
> 0.12, and ewald-rtol is the default 1e-5.
> I added the following line to "src/mdlib/ewald.c" just before "return
> energy;" in the "do_ewald" function and recompiled :
> This prints out the k-space contribution to the electrostatic energy at
> each step. As an example, at step 0 this it printed out 1008.472290
> After getting this I calculated the self contribution as follows. The
> logfile says that 1/beta (the Gaussian width) is 0.128065 nm, so beta =
> 7.808535 for this simulation. There are 33 water oxygens with a charge of
> -0.82 and 66 water hydrogens with a charge of 0.41. The following equation
> for the self term comes from section 4.9.1 of the manual (f = 138.935485):
> -f * beta / sqrt(pi) * [ (33)(-0.82)^2 + (66)(0.41)^2 ] = -20372.33 kJ/mol
> The logfile states for step 0 that Coulomb (Recip.) is -1.23120e+03
> kJ/mol, but this does not equal the total of the k-space and self
> correction terms:
> 1008.5 + -20372.3 = -19363.8
> I appreciate anybody's help with understanding what I'm missing here in
> understanding how GROMACS calculates the self correction or if Coul. Recip.
> is something else.
> Wes Barnett
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