[gmx-users] Re: fatal error when using Martini CG force field

[Justin A. Lemkul]

lammps lammps wrote:
> I use the gmx4.04 version.
> 
> The detail error information is as follows. May be there is a bug in 
> domain decompostion method because someone met this problem beforce.
> 
> --------------------------------
> Not all bonded interactions have been properly assigned to the domain 
> decomposition cells
> 
> A list of missing interactions:
>             G96Angle of   3704 missing      1
> 
> Molecule type 'DEN'
> the first 10 missing interactions, except for exclusions:
>             G96Angle atoms   62  129  130      global  5162  5229  5230
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.4
> Source code file: domdec_top.c, line: 341
> 
> Fatal error:
> 1 of the 13956 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
> --------------------------------------------
> 

Well, have you checked out the purpose of the -rdd option?  With a CG force 
field bonded interactions occur at longer distances than in a UA or AA force 
field.  Therefore, you may have to customize some of the mdrun options for use 
with DD before you can necessarily propose that the code is buggy.

-Justin

> 
> -- 
> wende
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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