[gmx-users] truncating LJ potentials

[Irem Altan]

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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