[gmx-users] 'SHAKE' : gromacs 4.0.7

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 20 23:56:40 CEST 2010

Ramachandran G wrote:
> Hello gromacs users:
>         I installed the new version of gromacs and tried to run 
> 'mdrun_mpi' in parrallel but it gives the error pasted below.
> When i switched the constrain from 'shake'  to 'lincs' it runs.   I know 
> 'shake' algorithm compilation was done but i don't why
> i am getting this error.  The error does not arise when i run it in 
> serial. Any help will be highly appreciated.
> ----------------------------------------------------------------------------------
> Program mdrun_mpi_d, VERSION 4.0.7
> Source code file: constr.c, line: 830
> Fatal error:
> SHAKE is not supported with domain decomposition and constraint that 
> cross charge group boundaries, use LINCS
> ----------------------------------------------------------------------------------------------

The error message is really quite explicit.  SHAKE + constraints between charge 
groups = failure.  You won't see any error in serial, because you can't run 
domain decomposition on a single processor.  If you want to use SHAKE, either 
run in serial, or perhaps you can try the old particle decomposition (mdrun 
-pd), but the results in both cases will certainly be slower than if you use 
LINCS and domain decomposition.


> best,
> Rama


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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