[gmx-developers] solvation free energy with couple-intramol set to 'no'

Erik Lindahl erik.lindahl at gmail.com
Thu Feb 27 14:50:10 CET 2020

Hi Vytas,

If you expect it's a problem, upload specific files to redmine (not just a
TPR, but complete input) where results ideally differ after just 1-5 steps,
and describe what you expect vs. what you get!



On Thu, Feb 27, 2020 at 2:46 PM Vytautas Gapsys <vgapsys at gwdg.de> wrote:

> Hey,
> I have encountered an unexpected outcome when calculating solvation free
> energies and using the option: couple-intramol = no
> The observation is that the forces, overall electrostatic energy and the
> final free energy depend on the rcoulomb cutoff, in spite of using PME.
> I speculate that the following might be happening: for this simulation,
> intramolecular interactions are replaced by explicit pair interactions,
> however, this apparently is done for both states - coupled and
> decoupled. This way, in the coupled state those intramolecular
> electrostatic interactions that are outside of the rcoulomb cutoff are
> counted twice (when using PME): once they are counted explicitly
> ignoring the rcoulomb cutoff, second time they appear in the reciprocal
> part of PME.
> This can be verified by extending rcoulomb up to the point where all the
> intramolecular interactions are within the rcoulomb cutoff. When
> extending the cutoff further from that point the overall electrostatic
> energy becomes rcoulomb independent.
> Such a dependence on rcoulomb is problematic, as tunepme can change
> rcoulomb value during runtime.
> Let me know if I am overlooking something and maybe this behaviour can
> be circumvented.
> Best Regards,
> Vytas
> --
> Vytautas Gapsys
> Project Leader at Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: vgapsys[at]gwdg.de
> Phone: +49 551 201-2310
> --
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Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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