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

[XAvier Periole]

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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