[gmx-users] Variation in free energy between GROMACS versions?

[Mark Abraham]

Hi,

On Wed, 24 Jul 2019 at 17:25, Kenneth Huang <khuang8 at student.gsu.edu> wrote:

> Hi all,
>
> I'm trying to implement a variation of  the simulated tempering procedure
> as described in a 2007 paper (Choosing weights for simulated tempering,
> Sanghyun Park and Vijay S. Pande, Phys. Rev. E 76, 016703) on GROMACS 2018,
> and am trying to verify that my implementation is correct compared to the
> system in the paper (Ala10). While I've managed to match a majority of the
> parameters that are described in the paper, the energy values I'm getting
> are all shifted about 3,000 kJ/mol relative to the ones in the paper.
>
> I'm not familiar enough with how mdrun itself has changed within GROMACS,
> and don't expect to fully be able to reproduce the results of the paper, so
> I was wondering if that large of a difference is expected? Considering that
> I'm using as many of the same settings as in the paper (ie, water model,
> forcefield, number of waters, thermostat, etc), is it unusual to see that
> magnitude of a change for a relatively simple system like Ala10 between an
> older and newer version of GROMACS? Or is this something that's expected,
> and I shouldn't worry to much about it?
>

There's a couple of philosophical questions here, but the important one for
the comparison is that such an old version of GROMACS probably didn't shift
the potential to zero at the cutoff (several MD packages still don't), and
even the values of the physical constants have been updated since then
(this was also a problem in comparing single-point energies between MD
packages in a SAMPL6? paper from Shirts & co). Given that the method used
reaction-field, you could probably make some measurements on things and
scale the potential shift by the number of short-range interactions...

Mark

Best,
>
> Kenneth
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