[gmx-users] Force-switch algorithm

[Mark Abraham]

Hi,

On Tue, Jan 5, 2016 at 4:46 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/4/16 10:41 PM, Pallavi Banerjee wrote:
> > Hi Mark,
> >
> > Thank you for your reply.
> >
> > I want to implement this wacky idea because a part of the potential of
> the
> > system needs to be input in a tabulated form (referring to Iterative
> > Boltzmann Inversion) and the other part (solvent-solvent) interaction is
> > defined by sigma and epsilon, which I again input in the form of a table
> > since GROMACS does not  support both tabulated and non-tabulated at the
> > same time.
> >
> > So, then, am I right to understand that eqn 4.28 of manual-5.1 is the
> > functional form of potential of the force-switch method, and that there
> is
> > no documentation provided for potential-switch?
> >
>
> It may not be in the GROMACS manual, but is it not the same as what is in
> Steinbach and Brooks JCC (1994) 15: 667-683, like the force-switch is?
> This is
> the CHARMM potential switching, which should be the same, IIRC.
>

Thanks, but
https://github.com/gromacs/gromacs/blob/master/src/gromacs/gmxlib/nonbonded/nb_generic.cpp#L137
suggests
they are not the same.

Mark


> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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