Don't know about the missing interactions ... never seen this in any
of the
gmx versions using Martini ...
for the error you should increase the -rdd to 1.4/1.5 nm
On May 13, 2009, at 4:36 PM, maria goranovic wrote:
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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