Re: [AMBER] Periodic boundary conditions and N_OF_BONDS_COLVAR

From: Feng Pan <>
Date: Wed, 13 Jun 2018 00:04:15 -0400

Hi, Hugo

The N_OF_BONDS should be good in PBC during the run.
The problem will happen when you do the restart run with bad
structure, so just do the image of the structure using cpptraj
before every restart run. Then the PBC problem should be solved.


On Tue, Jun 12, 2018 at 9:51 PM, Hugo Macdermott-Opeskin <> wrote:

> Dear All
> I have been having some trouble trying to run a set of simulations
> involving the coordination number of water with an ion using ABMD and the
> N_OF_BONDS colvar from nfe_colvar.f90.
> I noticed a significant disagreement with values that I computed from the
> trajectory using a python script and those output by the ABMD code. I then
> delved into the code and found that the N_OF_BONDS colvar does not compute
> distances using PBCs. This would normally not be a problem however as water
> can move quickly over the PBC, an incorrect ( as far as I can tell) value
> is obtained. Has anyone else had this problem?
> I have a fix for this using a number of functions written into
> nfe_colvar.F90 and some I have written myself, but they are pretty ugly
> and am I am struggling to validate my code.
> Any help or suggestions would be greatly appreciated.
> Cheers
> Hugo
> _______________________________________________
> AMBER mailing list

Feng Pan
North Carolina State University
Department of Physics
AMBER mailing list
Received on Tue Jun 12 2018 - 21:30:01 PDT
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