[gmx-users] truncating LJ potentials

[Irem Altan]

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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