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

From: Rohit Modee (rohit.modee_at_research.iiit.ac.in)
Date: Wed Aug 15 2018 - 04:34:52 CDT

yes, I am doing NPT REMD.

langevinPistonTarget 1.01325

dimesnsions of box
# Periodic Boundary Conditions
cellBasisVector1 51.579999923706055 0 0
cellBasisVector2 0 51.4640007019043 0
cellBasisVector3 0 0 51.75699996948242
cellOrigin 0.225006103515625 0.10952535271644592 -0.10641514509916306

MARGIN 1.0
PMEGridSpacing 1.0

----- Original Message -----
From: "Norman Geist" <norman.geist_at_uni-greifswald.de>
To: namd-l_at_ks.uiuc.edu, "Rohit Modee" <rohit.modee_at_research.iiit.ac.in>
Sent: Tuesday, August 14, 2018 11:58:06 AM
Subject: AW: namd-l: Periodic cell has become too small for original patch grid

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 : Wed Dec 11 2019 - 23:20:09 CST