Re: [AMBER] N_OF_BONDS colvar and PBC

From: Feng Pan <>
Date: Sun, 1 Aug 2021 23:20:25 -0400


I have fixed the bug and pushed the merge request.
Thanks to Hugo for finding and fixing this bug.


On Fri, Jul 30, 2021 at 9:25 PM David A Case <>

> On Sat, Jul 31, 2021, Hugo Macdermott-Opeskin wrote:
> >I wanted to raise the fact that the NFE colvar N_OF_BONDS does not compute
> >distances (and hence coordination numbers) under the nearest image
> >convention. I ran into this problem when I was trying to compute some
> >coordination numbers for an ion in water, and getting some strange values.
> >
> >Myself and Feng Pan wrote a patch to nfe_colvar.F90 that uses the nearest
> >image convention (a few very simple changes). I thought you all might be
> >interested and I can send source code if you like.
> If Feng has time, the easiest would be to submit a merge request to
> But otherwise, send the patch file to me, and I'll
> try to take care of it.
> Thanks for looking into this. Apologies if an earlier fix got lost.
> ....dac
> _______________________________________________
> AMBER mailing list

Feng Pan
Florida State University
Department of Statistics
AMBER mailing list
Received on Sun Aug 01 2021 - 20:30:02 PDT
Custom Search