[gmx-users] Domain decomposition in FEP

[Justin A. Lemkul]

Alexey Zeifman wrote:
> Dear all,
> 
> I'm trying to run FEP calculation of the ligand in the protein in water. 
> Performing NVT-dynamics for Lennard-Johnes perturbation using soft core 
> results in the following error:
> 
> There is no domain decomposition for 20 nodes...
> 
> I've checked out the log-file and found this:
> 
>  >Initial maximum inter charge-group distances:
>  >    two-body bonded interactions: 1.474 nm, Bond, atoms 4371 4391
>  > multi-body bonded interactions: 0.522 nm, Ryckaert-Bell., atoms 3747 3756
>  >Minimum cell size due to bonded interactions: 1.621 nm
>  >Guess for relative PME load: 0.29
>  >Will use 20 particle-particle and 12 PME only nodes
>  >This is a guess, check the performance at the end of the log file
>  >Using 12 separate PME nodes
>  >Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>  >Optimizing the DD grid for 20 cells with a minimum initial size of 
> 2.026 nm
>  >The maximum allowed number of cells is: X 3 Y 3 Z 3
>  >
> ->------------------------------------------------------
>  >Program mdrun_mpi, VERSION 4.5.1
>  >Source code file: domdec.c, line: 6428
> 
>  >Fatal error:
>  >There is no domain decomposition for 20 nodes that is compatible with 
> the given box and a minimum cell size of 2.02621 nm
>  >Change the number of nodes or mdrun option -rdd or -dds
>  >Look in the log file for details on the domain decomposition
>  >For more information and tips for troubleshooting, please check the 
> GROMACS
>  >website at http://www.gromacs.org/Documentation/Errors
> ->------------------------------------------------------>
> 
> I understand that distance of 1.474 nm is rather big for bond! BUT I 
> can't find such a distance between atoms 4371 4391. The fragment of 
> gro-file for such index interval looks like this:
> 
>   640LIG     C4 4371   2.897   3.416   3.072
>   640LIG     N3 4372   3.296   3.109   3.434
>   640LIG     N6 4373   3.416   2.999   3.595
>   640LIG     C6 4374   2.696   2.762   3.601
>   640LIG     C7 4375   3.025   3.232   3.150
>   640LIG     C8 4376   3.208   3.142   3.338
>   640LIG     C9 4377   2.758   2.644   3.649
>   640LIG    C10 4378   2.767   2.884   3.595
>   640LIG     N4 4379   3.319   2.826   3.731
>   640LIG    C11 4380   2.968   2.768   3.677
>   640LIG    C12 4381   2.894   2.648   3.686
>   640LIG    C13 4382   2.901   2.887   3.638
>   640LIG     N5 4383   3.100   2.766   3.707
>   640LIG    C14 4384   3.420   2.908   3.693
>   640LIG     O1 4385   3.018   3.627   3.068
>   640LIG    C15 4386   3.028   3.095   3.182
>   640LIG    C16 4387   3.123   3.049   3.275
>   640LIG     O2 4388   2.566   2.759   3.559
>   640LIG     O3 4389   2.699   2.993   3.545
>   640LIG     O4 4390   2.680   2.530   3.655
>   640LIG    C17 4391   2.791   3.426   3.184
>   640LIG    C18 4392   2.834   3.453   2.937
> 
> and the actual distance is 1.55 A - quite OK for single C-C bond.
> 
> And another interesting fact is that it doesn't occur during FEP 
> calculation of the same system without soft-core and aimed at only 
> charge perturbation.
> 
> I will appreciate any help regarding this.
> 

The general information about this error can be found at:

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

The DD setup is based on a host of factors.  Seeing a complete .mdp file would help.

-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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