[gmx-developers] problem with particle decompostion and with gromacs 4.6.3

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 3 17:36:02 CEST 2013

On Thu, Oct 3, 2013 at 5:21 PM, Floris van Eerden <f.j.van.eerden at rug.nl>wrote:

> Dear reader,
> This post describes two different problems while I was trying to run a
> protein monomer.
> 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 runs
> normal.
> However when I switch to particle dynamics the membrane starts buckling
> heavily, resulting in a completely folded membrane.

Other than the range of non-bonded interactions, is there anything
noteworthy in the topology or run setup? E.g. restraints, vsites, md-vv,
replica exchange, free-energy... The most likely problem is some feature
nobody ever tested / intended to work with PD. This is part of why PD is on
the chopping block for 5.0.

> This is in Gromacs 4.5.5 and 4.5.3

Please try a 4.5.7 run, so we can eliminate the years of accrued bug fixes
as the source of the problem :-)

> 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?

Some more information about your simulation would be good, but we'd
probably like you to open an issue at redmine.gromacs.org so you can attach
.tpr + preparation files as a tarball there.


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