[gmx-users] genconf and bonded interactions

Fabio Affinito f.affinito at cineca.it
Tue Jul 26 15:59:14 CEST 2011

Hi all,
I used genconf because I wanted to replicate a membrane with ion channel 
on the xy plane:
genconf -f conf.gro -o out.gro -nbox 2 2 1

Then I edited by hand the .top file where I modified the number of 
molecules in the system.

When attempting to run, disregarding the number of processors, the mdrun 
crashes because domain decomposition fails.
Looking with attention to the log I find this:
> 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: 30.871 nm, LJ-14, atoms 193657 193660
>     multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659
>     Minimum cell size due to bonded interactions: 33.959 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: 0.44
>     Will use 2304 particle-particle and 1792 PME only nodes
>     This is a guess, check the performance at the end of the log file
>     Using 1792 separate PME nodes
>     Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>     Optimizing the DD grid for 2304 cells with a minimum initial size of 42.448 nm
>     The maximum allowed number of cells is: X 1 Y 1 Z 0

Now, I'm wondering why do I have such big bond interation length.. 31nm!
I guess that the problems in the DD arises from this.

Can you give me some suggestions?

Thanks in advance,


Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198

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