Re: Separate switchdist for electrostatic interactions

From: Fotis Baltoumas (
Date: Mon Nov 21 2016 - 09:54:33 CST


When you run Martini simulations with NAMD, you should enable
"MartiniSwitching on" in your configuration file.

This, essentially, does what you ask: it enables the use of different
switchdist options for Lennard-Jones and Coulomb electrostatics. The
switchdist that can be set in the configuration file is actually to
describe the option for LJ interactions, while the coulombic switchdist
is automatically set to 0 (this is hardcoded in the NAMD source and
enabled with MartiniSwitching).

In other words, in your MARTINI configuration file you should include
the following:

# Force-Field Parameters
exclude 1-2
1-4scaling 1.0
cutoff 12.0
martiniSwitching on
PME off
switching on
switchdist 9.0
pairlistdist 14
dielectric 15.0

All of this is explained in more detail in the Residue-Based
Coarse-Graining tutorial files (although, technically, they SHOULD be
part of the User's Guide, so that people know how the force field is
ACTUALLY implemented in NAMD):

Good luck,


On 11/21/2016 02:17 PM, Peter Mawanga wrote:
> Hello everyone
> Is it feasible to use different /switchdist/ for LJ and electrostatic
> interactions in *Martini* simulations? I would like to switch LJ from
> say 9 Å and electrostatics from 0 Å to final /cutoff/ distance.
> htp://
> <>
> As per the NAMD literature available, this should be possible, but
> cannot figure out how to implement the same:
> Please suggest some way of doing so if it can be done.
> Cheers
> Peter

Fotis A. Baltoumas
Phd Candidate, Bioinformatics Postgraduate Programme
Department of Cell Biology and Biophysics
Faculty of Biology, University of Athens
Panepistimiopolis, Athens 157 01, GREECE
email :

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