[gmx-users] genconf and bonded interactions

[Justin A. Lemkul]

Fabio Affinito wrote:
> This is the mdrun output:
> 
> Initializing Domain Decomposition on 4096 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 30.031 nm, LJ-14, atoms 40702 40705
>   multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704
> Minimum cell size due to bonded interactions: 33.035 nm
> Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm
> Estimated maximum distance required for P-LINCS: 1.139 nm
> Guess for relative PME load: 0.43
> Will use 2400 particle-particle and 1696 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 1696 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 2400 cells with a minimum initial size of 
> 41.293 nm
> The maximum allowed number of cells is: X 0 Y 0 Z 0
> 
> -------------------------------------------------------
> Program mdrun_mpi_bg, VERSION 4.5.4
> Source code file: domdec.c, line: 6438
> 
> Fatal error:
> There is no domain decomposition for 2400 nodes that is compatible with 
> the given box and a minimum cell size of 41.2932 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 

This is bizarre.  Did you fix the periodicity of the original coordinate file 
(conf_start.gro) and rebuild the system, or did you try to run trjconv on the 
replicated system?  The former is the correct approach.

-Justin

-- 
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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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