[gmx-users] martini simulation problem with unsaturated lipid

Berk Hess gmx3 at hotmail.com
Fri Sep 25 13:35:29 CEST 2009

I think the text below "Fatal error:" explains pretty clearly why this interaction is missing.


Date: Fri, 25 Sep 2009 13:04:28 +0200
From: mariagoranovic at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] martini simulation problem with unsaturated lipid


I get this error while running Martini:

A list of missing interactions:
            G96Angle of   1280 missing      1

Molecule type 'DUPC'
the first 10 missing interactions, except for exclusions:

            G96Angle atoms    3    5    6      global   135   137   138

Does this mean that some terms are reallly missing?

Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 4040 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck

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