[gmx-developers] problem with particle decompostion and with gromacs 4.6.3
Floris van Eerden
f.j.van.eerden at rug.nl
Thu Oct 3 17:21:32 CEST 2013
This post describes two different problems while I was trying to run a
The first problem is that I get completely different results when I run
a system with particle decomposition or domain decomposition.
I simulate a coarse grained protein monomer embedded in a lipid bilayer
and solvated in water+ions. When I use domain decomposition the system
However when I switch to particle dynamics the membrane starts buckling
heavily, resulting in a completely folded membrane.
This is in Gromacs 4.5.5 and 4.5.3
I tried to reproduce these errors in Gromacs 4.6.3, but here my
simulations kept crashing. When i used particle dynamics I get a lot of
lincs warnings followed by a segmentation fault and when i use domain
decomposition it crashes with a 'software inconsistency error: some
particles seem to be assignment multipe times' (run on 8 cores with rdd
set to 1.8). When I use only one thread (-n1 ) I get an segmentation
fault. These while I can run these simulations without any problem
(except the buckling) on gromacs 4.5.5. It does not matter if the tpr
file is generated with gromacs 4.6.3 or gromacs 4.5.5.
Has anybody an idea what might be the problem?
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