Re: nitrogen in namd

From: Marco Sant (
Date: Sun Jul 31 2011 - 05:47:18 CDT

Dear all,
I sincerely thank you for your answers!!

Can anybody give me some information on "lonepair" or "DRUDE"?

On the reasons to use the charges:
I am a post-doc writing an article regarding N2 dynamics in ZIF8; we have already a flexible force field with partial charges computed via DFT which took a fair amount of work to the group, then it would not be nice to use a sorbate with no charges in a sorbent modeled with such a detail. And writing in the article that I couldn't use the charges for the sorbate because the package couldn't do it sounds a bit upsetting :)

Of course I can either do it without charges or use another package, still I will first try my best to do it in NAMD using the charges.

Regarding your suggestions:
the simulation cannot be done simply placing a dummy bonded particle in the middle between the N atoms. To have reasonable dynamics (correct momentum of inertia for example) this atom would need a very small mass (zero is not possible). But then the simulation crashes because:
at first step the dummy charged particle feels a force due to the electrostatics and then, because its mass is very small, the force will produce a big acceleration which will result in a too big velocity that will crash NAMD. The key point is that the bonded force, between the dummy atom and the N atoms, will act only at next step after a displacement occurs. But at that point the dummy particle has already moved too much or crashed the simulation. I have tested this.

After the suggestion of Jim Philips i looked a bit at the code and saw lines regarding "lonepairs" and "DRUDE". But I found no documentation on this, it seems like this part is currently under development.

Any further suggestion would be welcome!!

I confirm that the negative charge is on the Nitrogens and the positive in the center of mass. At least in the TraPPE model of N2:

Thanks a lot,

--- Mer 27/7/11, Jim Phillips <> ha scritto:

Da: Jim Phillips <>
Oggetto: Re: namd-l: nitrogen in namd
A: "Marco Sant" <>
Data: Mercoledì 27 luglio 2011, 22:07

That would be a "lone pair" in the NAMD code.  You'll need to modify code such as HomePatch::reposition_all_lonepairs() to recognize and deal with bisector lone pairs (the position calculation is trivial of course).

For a first cut you could treat the partial charges as zero, particularly if the partial charges for your porous material are small.  I'm sure there is a chemist on the list who will respond that this is either sufficient or useless, but I can't guess which it would be.


On Wed, 27 Jul 2011, Marco Sant wrote:

> Good morning,
> I would like to compute the self-diffusion of N2 within a porous material using namd.
> I need to place a point charge on each N atom plus a point charge in the center of mass of the N2 molecule. In other words, I need something like a "virtual site" or a "dummy atom" having charge but not mass and being placed in the center of the N2 molecule.
> shape of N2
> N---------N
> (-)  (+)  (-)
> Which is the best way to do this with NAMD?
> Thanks a lot for the attention,
> best regards,
> M&B

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