Possibility of modifying the non-bonded terms of the potential

From: Ali Emileh (ali.emileh_at_gmail.com)
Date: Fri Jul 08 2011 - 16:58:44 CDT

Hi all,

Is it possible to cancel out VdW/Coulomb interactions of the force field
(more specifically CHARMM) independently in NAMD?
The closest thing I could find in the documentations was the
*"nonbondedScaling"
*parameter but from what I can understand it
affects both terms together. The only other way I can imagine is to scale
them both to zero and then add the intended term
using TclForces (vaguely, I'm not even sure if that's possible) but I think
this will hit the performance very badly and I'd like to
avoid that. But if that's the only way, well, then it won't matter as I'm
not intending to run very long simulations (1 ps most).

The only thing I could find in the mailing list was this :
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12961.html
but is it possible to do this for a protein system with all the different
atom types?

I'd appreciate any guidance/suggestions.

Thank you
Ali

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