[gmx-developers] Flat-bottom potentials

Jochen Hub jhub at gwdg.de
Mon Mar 5 09:24:52 CET 2012

OK, since there are obviously no preferences for how to implement 
flat-bottom potentials, I'll just use new function types and submit the 
implementation to Gerrit (and hope that it is acceptable).


Am 3/2/12 12:23 PM, schrieb Jochen Hub:
> Hi developers,
> I would (finally) like to implement some flat-bottom quadratic
> potentials into Gromacs. They are useful for many applications, but so
> far I usually implemented them as more or less dirty hacks, which of
> course never made it into the main branch. Berk, David and me talked
> about that topic already years ago, and now I would like to continue
> this debate.
> I think the flat-bottom quadratic potentials should allow:
> 1) different geometries:
> - spherical (e.g. to avoid evaporation from a spherical droplet)
> - cylindrical in x-y plane, but free in z (needed to compute PMFs for
> membrane channels, to keep the solute aligned with the channel pore)
> - 1D, e.g. to keep a layer of some thickness stable
> 2) different reference positions. This is important if you compute PMFs
> for mutimeric membrane channels, where you want to have a cylindrical
> flat-bottom quadratic potential at each monomer.
> I can think of two ways to implement them:
> a) not preferred: into the pull code. AFAIK, that would not allow
> different reference positions at the moment (tell me if I am wrong).
> b) preferred: New function types (ft) for the [ position_restraints ]
> section in the topology. So ft=1 would be the normal posres, and ft 2,
> 3, 4 5, 6 could be for spherical, cylindrical in the xy plane, and 1D in
> X, Y, and Z, respectively. So ft>1 would ask for one additional
> parameter r which gives the radius/half-width of the flat bottom. Only
> one force constant would be required for the flat-bottom potential.
> Would you agree with that? Please let me know.
> Cheers,
> Jochen

Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189

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