[gmx-users] BUG: Free energy calculation

[Justin A. Lemkul]

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

-- 
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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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