From: Meric Ayse Ovacik (movacik_at_KU.EDU.TR)
Date: Mon Jul 12 2004 - 03:25:04 CDT
I overcame this problem by increasing the distance between the protein
molecule and water while generating waterbox around the protein. That
Ayse Meric Ovacik
----- Original Message -----
From: "Shirley Hui" <shirleyhui_at_alumni.uwaterloo.ca>
Sent: Friday, July 09, 2004 11:24 PM
Subject: namd-l: Common Problem!: Periodic cell has become too small for
original patch grid!
> I have been having many many problems with my simulations crashing after
> 2000 time steps due to:
> 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 noticed that this is a common problem. I have consulted the mailing
> and user guide and I found in the user guide, the following:
> "Margin violations mean that atoms that are in non-neighboring patches may
> be closer than the
> cutoff distance apart. This may sometimes happen in constant pressure
> simulations when the cell
> shrinks (since the patch grid remains the same size). The workaround is to
> increase the margin
> parameter so that the simulation starts with fewer, larger patches.
> Restarting the simulation will
> also regenerate the patch grid."
> So, if I want to reset the margin, what is a good value for the margin?
> much do you increase it by?
> Thanks for any information,
> Shirley hui
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