[gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error

Berk Hess gmx3 at hotmail.com
Wed Nov 19 09:28:23 CET 2008


The LJ-14 interaction is a two-body interaction,
one of which is apparently at a distance longer than the non-bonded cut-off.
mdrun determines the communication distances when starting
the simulation, see the md.log file for details.
Apparently all your bonded interactions are initially within
the non-bonded cut-off distance, but become longer
during the run.

You can set the bonded communication distance (as hinted
in the error message) with the mdrun option -rdd.
1 nm might already be enough, but the distance will no affect
the performance significantly (unless it prohibits certain
dd grid setups).


Date: Wed, 19 Nov 2008 00:43:48 +0000
From: lastexile7gr at yahoo.de
To: gmx-users at gromacs.org
Subject: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew	error


(I remind you that my initial system is a monoclinic crystal, which is a sub categorie to triclinic boxes)

compiling gromacs 4.0.2 with fftw3.2 and having the skew problem, now even in less steps than before, I face this:

Not all bonded interactions have been properly assigned to the domain decomposition cells

A list of missing interactions:
               LJ-14 of  15408 missing      1

Molecule type 'molec'
the first 10 missing interactions, except for exclusions:
               LJ-14 atoms   44   55           global  1881 

Program mdrun, VERSION 4.0.2
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 24208 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.74473 nm) or
the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck

I'm using the switch spline option and the second cut-off is the one I'm using. I do not know how the first cut-off is calculated. 

Also I get messages about : correcting invalid box during the simulation.

Should I change anything to my files and/or to the options of grompp, and if the answer is affirmative which of them?

Thank you,

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