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.
-Justin
best,
Rama
--
========================================
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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