Excluding non bonded interactions between segments

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Wed Apr 02 2014 - 07:40:29 CDT

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 (http://pubs.acs.org/doi/abs/10.1021/ct400617g).
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,

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