Re: Excluding non bonded interactions between segments

From: Jérôme Hénin (
Date: Wed Apr 02 2014 - 08:09:21 CDT

Hi Fotis,

NAMD will honor non-bonded exclusions defined in the PSF file, but you don't have to edit that file by hand. You can generate the exclusions as you would for an alchemical FEP simulation using Alchemify:


----- Original Message -----
> Dear NAMD Community,
> Is it possible to run a simulation in NAMD in which non bonded
> interactions between two selections/segments are excluded or ignored? (for
> example, between a membrane and a protein). If so, can it be done through
> the configuration file, or do I need to edit the psf?
> Some context to what I am asking. I am trying to replicate the recently
> published "Going Backward" method on constructing all atom models from
> MARTINI CG simulations (
> This method has been designed for GROMACS, and I am attempting to do the
> same through NAMD (since I performed my CG simulation with the NAMD
> nightly build). Most of the procedure is fairly straightforward and can be
> easily adapted to NAMD, except for the first simulation step, which
> involves energy minimization where non-bonded interactions between atoms
> in selected groups (in my case, the protein and the membrane) are
> excluded. In GROMACS this is done through the "energygrps" and
> "energygrp_excl" options. Does NAMD have a similar feature?
> Thank you,
> Fotis

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