[gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error

[Claus Valka]

Hello,

(I remind you that my initial system is a monoclinic crystal, which is a sub categorie to triclinic boxes)

compiling gromacs 4.0.2 with fftw3.2 and having the skew problem, now even in less steps than before, I face this:

Not all bonded interactions have been properly assigned to the domain decomposition cells

A list of missing interactions:
               LJ-14 of  15408 missing      1

Molecule type 'molec'
the first 10 missing interactions, except for exclusions:
               LJ-14 atoms   44   55           global  1881  1892

-------------------------------------------------------
Program mdrun, VERSION 4.0.2
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 24208 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.74473 nm) or
the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck

I'm using the switch spline option and the second cut-off is the one I'm using. I do not know how the first cut-off is calculated. 

Also I get messages about : correcting invalid box during the simulation.

Should I change anything to my files and/or to the options of grompp, and if the answer is affirmative which of them?

Thank you,
Nikos




      
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