Re: Periodic cell has become too small for original patch grid

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 13 2018 - 07:00:35 CDT

The error means that the original subvision of the unit cell into patches
(used to divide computation among nodes) cannot be used any more because
the unit cell has shrunk too much. Did you equilibrate the system before
starting REMD?

On Mon, Aug 13, 2018 at 4:27 AM Rohit Modee <rohit.modee_at_research.iiit.ac.in>
wrote:

> Dear All,
>
> I am running REMD simulations. have divided 100 ns into 5 jobs of 20 ns
> each.
> my job0 of 20 ns is complete but when i start job1 from checkpoint files
> from job0 it gives me following error at 22ns
> Reason: REPLICA 9 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.
>
> can some one please explain what this error technically means.
>
> i am already using margin of 1 A my water box is cubic with l=50 A
>
> in log file i get this value "PME GRID DIMENSIONS 54 54 54" why is
> this 54 instead of 50.
>
> what effect will it have if
> 1. I restart job1 with margin as more than 1.
>

You are in the best position to answer this.

>
> regards,
> Rohit
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

This archive was generated by hypermail 2.1.6 : Sun Sep 22 2019 - 23:19:51 CDT