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From: Jinasena Hewage (jwhewage_at_gmail.com)
Date: Thu Jul 02 2015 - 10:48:18 CDT

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