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

[albitauro at virgilio.it]

I have indeed large forces and the simulation stops after step 5...

****************************************************************************

----Messaggio originale----

Da: gmx3 at hotmail.com

Data: 25-set-2009 12.27 PM

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

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





-->

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.

Berk


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.

Thanks

AM



----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?

Berk


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

Hi,

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?
Thanks!

AM

 		 	   		  
Express yourself instantly with MSN Messenger! MSN Messenger



 		 	   		  
What can you do with the new Windows Live? Find out




 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090925/4ffe8a51/attachment.html>