From: Aron Broom (broomsday_at_gmail.com)
Date: Sat Oct 05 2013 - 07:10:17 CDT
I don't believe you need to re-minimize. As I understand it the error is
relating to a problem in how the parallelization of the computations is
allocated and not any actual numerical error with your simulation, so even
the last step should produce a system that is the same as if there was no
But, I imagine the error occurred very early in the simulation? If so,
it's not going to hurt to re-minimize and then start equilibrating again.
On Sat, Oct 5, 2013 at 3:56 AM, Vidhya Sankar <vidhyasankar7928_at_yahoo.com>wrote:
> Dear Namd user I aa Beginner of Namd simulation
> When i Run Simulation I ahve got the Following 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 have searched the Namd Mailing List and Finally I have Restarted the
> Simulation from Latest Configuration and steps Before it shows Patch grid
> But My question is Should i Do the Minimization or Not when i restart
> the Simulation ?
> Thanks in Advance
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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