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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 14 2018 - 01:28:06 CDT

Are you doing NPT remd?
What target pressure are you using?
 What are the box dimensions?

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Rohit Modee
> Gesendet: Montag, 13. August 2018 10:26
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Periodic cell has become too small for original patch grid
>
> 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.
>
> regards,
> Rohit

This archive was generated by hypermail 2.1.6 : Mon Nov 18 2019 - 23:20:03 CST