Re: About restaring Simulation

From: Aron Broom (
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 <>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
> error
> 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

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:44 CST