[gmx-users] Domain decomposition in FEP

[Alexey Zeifman]

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.

Alexey Zeifman

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