[gmx-users] default -rdd with distance restraints seems too large

Christopher Neale chris.neale at mail.utoronto.ca
Thu Oct 17 14:54:09 CEST 2013

Indeed, sorry that I didn't notice that, Mark. Looks as if the two-body bonded interaction gets multiplied by 1.1/0.8 so I suppose that this is working as it should.

It's a shame that long distance restraints limit the parallalization so much, but it is understandable. Thanks for helping me with this.


-- original message --

Initializing Domain Decomposition on 8 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: 2.636 nm, Dis. Rest., atoms 1701 4425
  multi-body bonded interactions: 0.479 nm, CMAP Dih., atoms 1062 1081
Minimum cell size due to bonded interactions: 2.899 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.172 nm
Estimated maximum distance required for P-LINCS: 1.172 nm
Using 0 separate PME nodes, as there are too few total
 nodes for efficient splitting
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 3.624 nm
The maximum allowed number of cells is: X 1 Y 1 Z 2

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