[gmx-users] error during equilibriation

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> 
> Dear all,
> am trying to simulate a cnt double  walled  in tip 4p water .had no 
> problem till minimization but during equilibri i got the following 
> error....any suggestions please.
> *A list of missing interactions:
>                Angle of   2097 missing     14
>       Ryckaert-Bell. of   1286 missing     12
>                LJ-14 of   2801 missing      8
>           exclusions of  31870 missing     14
> 
> Molecule type 'ICE'
> the first 10 missing interactions, except for exclusions:
>                LJ-14 atoms   79  299           global    79   299
>                LJ-14 atoms  165  299           global   165   299
>                Angle atoms  167  207  299      global   167   207   299
>       Ryckaert-Bell. atoms  167  207  299  285 global   167   207   
> 299   285
>       Ryckaert-Bell. atoms  173  175  285  299 global   173   175   
> 285   299
>                LJ-14 atoms  173  299           global   173   299
>                LJ-14 atoms  173  352           global   173   352
>                Angle atoms  175  285  299      global   175   285   299
>                Angle atoms  175  285  352      global   175   285   352
>       Ryckaert-Bell. atoms  175  285  299  207 global   175   285   
> 299   207
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.3
> Source code file: domdec_top.c, line: 356
> 
> Fatal error:
> 48 of the 46602 bonded interactions could not be calculated because some 
> atoms involved moved further apart than the multi-body cut-off distance 
> (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for 
> pairs and tabulated bonds also see option -ddcheck
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors*
> 

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Without seeing an .mdp file, and perhaps the topology, there's little else to 
suggest.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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