[gmx-users] genconf and bonded interactions
f.affinito at cineca.it
Tue Jul 26 15:59:14 CEST 2011
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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