Re: Possibility of modifying the non-bonded terms of the potential

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Jul 09 2011 - 03:34:36 CDT

Hi Ali,

To cancel the terms separately, you can:
a) use VMD to make a modified PSF file with zero charges
b) make a modified parameter file where the epsilon parameter is
zeroed out in the NONBONDED section

If you want a custom vdW term, just use tabulated potentials.

Cheers,
Jerome

On 8 July 2011 23:58, Ali Emileh <ali.emileh_at_gmail.com> wrote:
> 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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