R: RE: [gmx-users] Tabulated potential - Problem

Berk Hess gmx3 at hotmail.com
Fri Sep 25 14:27:18 CEST 2009

Your system could be unstable.
You can check for large forces with mdrun -pforce
I don't know what a reasonable range of forces is, you can try 5000.
If you have instabilities, you should get large forces printed
before you get the fatal error.


Date: Fri, 25 Sep 2009 14:10:08 +0200
From: albitauro at virgilio.it
To: gmx-users at gromacs.org
Subject: R: RE: [gmx-users] Tabulated potential - Problem

Unfortunately, my box sizes are not close to 23. I also carried out calculations switching off PBC or on much smaller systems. 
I received always the same error. 
I tried also a geometry optimization. It finished without warnings nor errors: anyway the potential energy changed only very slightly during the simulation with too large values.



----Messaggio originale----

Da: gmx3 at hotmail.com

Data: 24-set-2009 11.29 AM

A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>

Ogg: RE: [gmx-users] Tabulated potential - Problem

This is not nonsense, it is exactly what is says.
The distance between two atoms is more than 10 times as large as your table length.

Maybe you are somehow having issues with periodic boundary conditions.
Is you box size close to 23?


Date: Thu, 24 Sep 2009 12:32:36 +0200
From: albitauro at virgilio.it
To: gmx-users at gromacs.org
Subject: [gmx-users] Tabulated potential - Problem


I'm trying to carry out a CG simulation and I'm using
a tabulated potential for a bond stretching term.
My MD simulations stops immediately with the error message:

Program mdrun_mpi, VERSION 4.0.5
Source code file: bondfree.c, line: 1772

Fatal error:
A tabulated bond interaction table number 0 is out of the table range: r 23.678833, between table indices 12069 and 12070, table length 1020

This should mean that some distances are beyond table length (as reported in the manual) but this is
nonsense considering my input files and topology.

Do you have any suggestion?


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