[gmx-users] truncating LJ potentials

[Mark Abraham]

Hi,

The "only" thing you can do is define energy groups, and have a table per
kind of interaction between atoms from each energy group.

Mark

On Tue, Jul 12, 2016 at 11:15 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> Thanks. If I want to do this for only a subset of protein atoms (backbone
> atoms, for instance), what happens when calculating interaction between a
> side chain protein atom (with default LJ format) and a backbone atom? Is it
> possible to have the backbone atoms interact with the truncated LJ
> potentials within themselves only, while they interact with the default
> potentials with the side chain atoms?
>
> Best,
> Irem
>
> > On Jul 11, 2016, at 2:57 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > Hi,
> >
> > Tabulated interactions are the way to get such stuff done (but still
> > missing from the Verlet scheme).
> >
> > Mark
> >
> > On Mon, Jul 11, 2016 at 7:42 PM Irem Altan <irem.altan at duke.edu> wrote:
> >
> >> Hi,
> >>
> >> I’m trying to figure out how to truncate the LJ potentials at the
> >> repulsive part. I found a similar question and answer in the mail list
> from
> >> 2011:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__comments.gmane.org_gmane.science.biology.gromacs.user_37093&d=CwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=3joG0jg-sllprJjtyx4Rv-v2ObrvjzPOfs7Zkr6g1GE&s=rWlJ2Qf766zHprJEJaM9X5AzZwOKnyIikjcJJeZL-FY&e=
> >>
> >> Is the answer still the same? Has a newer/easier way of this been
> >> implemented since 2011?
> >>
> >> Best,
> >> Irem
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