[gmx-users] truncating LJ potentials

Wed Jul 13 10:19:08 CEST 2016

Hi,

Seems like you want

E(backbone-CN-atoms, backbone-CN-atoms) = truncated
E(backbone-CN-atoms, other) = normal
E(other, other) = normal

so you need just two energy groups, and a singletable for the modified
interactions (which will still use the LJ parameters for the atom types
involved). Note also that the bonds along the backbone will create
exclusions in the usual way for the force field.

Mark

On Wed, Jul 13, 2016 at 3:13 AM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> Just to make sure if I understood correctly: if I create energy groups as
> (i) Calpha, (ii) Cbackbone, (iii), Nbackbone, (iv) everything else, I
> should be able to achieve what I want, right?
>
> Best,
> Irem
>
> On Jul 12, 2016, at 5:35 PM, Mark Abraham <mark.j.abraham at gmail.com
> <mailto:mark.j.abraham at gmail.com>> wrote:
>
> 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<mailto:
> 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
> <mailto: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<mailto:
> 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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