[gmx-users] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing

maria goranovic mariagoranovic at gmail.com
Wed May 13 16:36:14 CEST 2009

Dear All,

I ran a POPC simuIation in gromacs 3.3.1 with the martini force field and it
ran fine. But I am getting the following error when I run it in gromacs
4.0.4. It seems there is some problem with the way the topology is built,
but I cannot find out what the problem is?

A list of missing interactions:
            G96Angle of   2395 missing      1

Molecule type 'POPC'
the first 10 missing interactions, except for exclusions:
            G96Angle atoms    9   10   11      global  1933  1934  1935

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

Fatal error:
1 of the 5532 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 pair
s and tabulated bonds also see option -ddcheck
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