Sabine Reisser wrote:
Hi Mark,
with FE, without PR : same error
without FE, with PR: stable
without FE, without PR: stable
I've never had this error before.
Logfile says:
[...]
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761
multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686
Minimum cell size due to bonded interactions: 3.675 nm
Using 0 separate PME nodes
Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm
The maximum allowed number of cells is: X 1 Y 1 Z 2
Domain decomposition grid 1 x 1 x 2, separate PME nodes 0
PME domain decomposition: 2 x 1 x 1
Domain decomposition nodeid 0, coordinates 0 0 0
[...]
Linking all bonded interactions to atoms
There are 55376 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: Z 1
The initial domain decomposition cell size is: Z 5.09 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.200 nm
two-body bonded interactions (-rdd) 4.213 nm
multi-body bonded interactions (-rdd) 4.213 nm
These quantities look very weird to me. They indicate interactions that are
very far apart are influencing one another. Can you provide a complete .mdp
file? It seems like some aspect of the free energy settings (perhaps
couple-intramol?) and DD aren't getting along. The other possibility is to try
particle decomposition instead of DD (i.e. mdrun -pd).
-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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