Hello Gromacs users and developers, I have a few questions concerning the calculation of the electrostatic forces in Gromacs.
Unfortunately I am not able to reproduce the electrostatic forces
computed by the gromacs code ( VERSION 4.0.99_DEAD_CVS_BRANCH_20090604
(double precision), compiled on MacOS X 10.5 using its native gcc and
no fortran compiler ) by a self written code , that also uses double
precision, though the energies derived with the different codes match
perfectly. To get an idea where the deviation stems from Berk already
gave me the hint to setup following configuration:
A positive charge is located at (5.0+a,5.0,5.0) and a negative charge
at (5.0-a,5.0,5.0) in a cubic box of size 10x10x10 and this setup for
the electrostatic forces with an arbitrary parameter a, that allows me
to control the strength of the interaction. Furthermore following
mdp-parameter were applied to achieve a very high accuracy of the Ewald
sum ( delta < 10^-18 kJ / (mol nm) compared to an infinite large cutoff ):
rlist=4.5
rcoulomb=4.5
rvdw=4.5
coulomb-type=ewald
knx=kny=knz=70
ewald_rtol=1.348768e-21 ( -> 1/beta=0.6666667 )
Now I checked different cases:
1. a = 2.5 -> only the reciprocal part of the Ewald sum is taken into
account and we have small terms in the sums:
In this case everything is perfect, apart from the forces in y and z
direction. The forces as well as the energies match up the last
digit.
2. a=2.0 -> both contribtions from direct and recipr. space and the
amount of the terms is much larger.
The energies also match perfectly, however the forces differ
already by an amount of 10^-2 kJ / (mol nm).
3. a=0.2 -> very large terms
Furthermore the energies fit perfectly, but the forces differ
significantly.
As a first resumee I have assumed the implementation of the calculation
of the direct forces is wrong. Than I checked the code and compared the
analog part in gromacs. To stay as compatible as much is also use
gmx_erfc() in my code.
The energies are derived by summing over all pairs within the cutoff.
In this routine also the forces are calculated and added to the involved
particles.
Unfortunately there are so many sources where an an error can easily be introduce. So at first I checked terms get lost during the summation of the forces. But then I would not obtain exactly the same energies like gromacs. To exclude the possibility of a wrong calculation of the direct forces I already compared the code lines for the force calculation in gromacs (src/mdlib/tables.c line 655) and the othercode, but they also match.
Can somebody give me an idea, where this deviations can arise from ? Obviously an increase of the forces yields significant differences. This can also be observed, when I decrease the box size and test case 1.). For a 4x4x4 box the deviation is as large as the actual force. Cheers, Flo Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !!
pgpNeWfhD3tEY.pgp
Description: PGP signature
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
