Re: NAMD support for lone pairs

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Mar 08 2019 - 18:18:28 CST

We have been able to run simulations with this type of lone pair using a nightly build for months now. Thanks again to Brian for getting it in so quickly!

Best,
JC

On Mar 8, 2019, at 3:14 PM, Brian Radak <brian.radak_at_gmail.com<mailto:brian.radak_at_gmail.com>> wrote:

This should be supported now for a valid PSF (did you try it and have it not work?).

The current lack of functionality is in the RTF parser inside psfgen, so that you cannot yet build these PSFs. I would recommend CHARMM-GUI for that purpose, although there are plans to support this in the future.

On Fri, Mar 8, 2019, 12:10 PM Tabitha Nobel <hydrargyrumate_at_gmail.com<mailto:hydrargyrumate_at_gmail.com>> wrote:
Hi Brian,

Thank you very much for your response. This might be a naive question, but if I have a chloro group with a lone pair generated from CGenFF, is there a way I can convert that to a currently supported format from NAMD?

Thank you,
Tabitha

On Fri, Mar 8, 2019 at 7:45 AM Brian Radak <brian.radak_at_gmail.com<mailto:brian.radak_at_gmail.com>> wrote:
Hi Tabitha,

As of 2.13 there should be full support for all lonepair types that exist in currently published/released CHARMM force fields, both fixed charge and Drude. This includes the "bisector" lonepairs on water and carbonyls as well as the "collinear" lonepairs most associated with halogens (e.g. chlorobenzene). Furthermore, the old "lonepair on" keyword should be essentially deprecated and instead auto-detected based on the PSF contents (it should be very obvious if this does not work). However, NAMD does not yet support all CHARMM compatible lonepairs because they are not defined in the PSF standard.

Cheers,
BKR

On Thu, Mar 7, 2019 at 9:27 PM Tabitha Nobel <hydrargyrumate_at_gmail.com<mailto:hydrargyrumate_at_gmail.com>> wrote:
Dear NAMD developers,

Are CGenFF lone pairs supported in NAMD version 2.13? This question is similar to the one asked here<https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2018-2019/0992.html>, but I saw in the release notes<https://www.ks.uiuc.edu/Research/namd/2.13/features.html> that there was improved lone pair support, and it wasn't clear to me whether that was only for the Drude force field.

Thank you,
Tabitha

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