[gmx-users] tables.xvg warning - error

Berk Hess gmx3 at hotmail.com
Thu Oct 30 16:00:47 CET 2008


The 4.0 pdf manual (unfortunately currently only available from the ftp site)
will tell you that in 4.0 you need to give V and F=-V' instead of V and V'' as in version 3.
It is good that I put in a check for the numerical derivative of V,
so the user is warned that the tables might be incorrect.


Date: Thu, 30 Oct 2008 14:35:31 +0000
From: lastexile7gr at yahoo.de
To: gmx-users at gromacs.org
Subject: [gmx-users] tables.xvg warning - error


In previous versions I do not get that error. My potential uses tables for non bonded intermolecular interactions. In gromacs-4.0 I get the following:

WARNING: For the 1131 non-zero entries for table 1 in table_CGAC_CGCNZ.xvg the forces deviate on average 222% from minus the 
numerical derivative of the potential

and in the end:

NOTE: Turning on dynamic load balancing

Step 8:
The charge group starting at atom 930 moved than the distance allowed by the domain decomposition (0.932308) in direction X
distance out of cell -34873385.214308
Old coordinates:    2.590    3.591    2.789
New coordinates: -34873382.919    0.319    1.806
Old cell boundaries in direction X:    2.298    3.455
New cell
 boundaries in direction X:    2.295    3.454

Program mdrun, VERSION 4.0
Source code file: domdec.c, line: 3440

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

Is this something I'm doing wrong or a bug?

Thank you,

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