[gmx-developers] Hacking domain decomposition for long range bonded terms.

XAvier Periole x.periole at rug.nl
Mon Nov 18 22:00:15 CET 2013


Following on the issue of long range bonded terms preventing the use of DD and before fixed using PD. 

We have looked into the groupcoord.c solution but are currently stuck. Our idea was to supplement at each step the local atom list of each node with the atoms involved in those long range bonded terms (total of six atoms). We have bypassed the check on the minimum DD box size (15 nm) by forcing the code to take the decomposition we choose. Here 2x2x2. 

Of course now mdrun crashes when getting to calculate those long range bonded interactions and complains that they are missing. The error message is given bellow. We have trouble finding where exactly the code determines which coordinates to communicate to each domain. 

Any suggestion or hint would be greatly appreciated.

XAvier and Manel.

A list of missing interactions:
                Bond of  60636 missing      1
       Improper Dih. of     12 missing      2

Molecule type 'rhodimmer'
the first 10 missing interactions, except for exclusions:
       Improper Dih. atoms  117  423  279 1066 global   117   423   279  1066
                Bond atoms  279 1066           global   279  1066
       Improper Dih. atoms  279 1066 1210  904 global   279  1066  1210   904

Program mdrun, VERSION 4.6.3
Source code file: /src/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393

Fatal error:
3 of the 103492 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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