[gmx-users] Coulomb barriers and Coulomb Softcore Potential

Michael Shirts mrshirts at gmail.com
Mon Aug 24 17:07:47 CEST 2015

Adjusting the soft core is a gigantic pain.  I wouldn't recommend it,
and it's likely not necesssary. What settings are you using now?  Note
that the manual describes how it is defined.

Can you post the alchemical-analysis output for N/N_k?  There's an
analysis quirk we are looking at where the correlation times are
measured to be longer than they actually are, though that is when LJ
is changing and coul is turned off.

Look at the time correlation for the variable that is changing -- does
it look stationary, or does it look like it's changing slowly, or has
just a few discrete steps?  If the autocorrelation time is slow, then
N/N_k actually is that long, and the code is doing it's job.

On Mon, Aug 24, 2015 at 9:55 AM, Andreas Mecklenfeld
<a.mecklenfeld at tu-braunschweig.de> wrote:
> Dear Gromacs-Users,
> I want to calculate the solvation free energy of water in an aqueous ionic
> solution and I'm using the Python tool "alchemical-analysis.py" by
> Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very
> high N/N_k ratio (up to 7000) while decreasing the electrostatic potential
> (Lennard Jones fully active).
> Considering energetic barriers, I would like to adjust the Coulomb Softcore
> Potential. Does this seem plausible and if so, how is the Coulomb Softcore
> Potential defined in Gromacs?
> Naden and Shirts provide a concept by equation (A.2) in "Linear Basis
> Function Approach to Efficient Alchemical Free Energy Calculations. 2.
> Inserting and Deleting Particles with Coulombic Interactions"
> (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula
> intended?
> Best regards,
> Andreas
> --
> M. Sc. Andreas Mecklenfeld
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> Technische Universität Braunschweig
> Institut für Thermodynamik
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