VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 02 2015 - 11:11:06 CDT

please post questions about NAMD to the NAMD mailing list. thanks.

On Thu, Jul 2, 2015 at 11:48 AM, Jinasena Hewage <jwhewage_at_gmail.com> wrote:
> I have been running protein in carbon nanotube inserted in hexagonal water
> cylinder. I am getting this error.
>
> Reason: FATAL ERROR: Periodic cell has become too small for original patch
> grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> Charm++ fatal error:
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> I tried following,
> 1) Instead of using Periodic boundary condition in .conf file, I used .xrc,
> but still getting same error.
> 2) I used the boundary lengths given in .txt file generated when I created
> the water cylinder even thought I increased the size of the cylinders, same
> problem is there.
> This run without any problem in NVT ensemble used in equilibration but
> production run with constant pressure doesn't work.
> I need your help please.
> Thank you
> Hewage
>
> Dr. Jinasena Hewage
> Senior Lecturer in Physical Chemistry
> (Current Position: Visiting Academic, Research School of Chemistry,
> Australian National University)
> Department of Chemistry
> University of Ruhuna
> Matara, Sri Lanka
> (+94) 071 4500 389 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.