[gmx-users] mdrun error

[Elton Carvalho]

Dear Golnaz,

Depending on how your system is set up, you have a few options, listed
here in the order I would try them (knowing no details about your
system):

1) If you have less than, say, 100~500 atoms per CPU core (depending
on your network), use less nodes to run the simulation. The
parallellism starts getting worse at this point:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Approaching_the_scaling_limit

2) If your box is high enough on the z direction, try mdrun -dd 1 1 4
(with 4 here being the number of nodes you're running on. Take into
account step 1 above), so that you don't have to do DD in the short
dimensions.

3) Enlarge your box if it physically makes sense: What's the
surfactant concentration you're aiming for? Note you'll have to
replicate rour graphene sheet so it fills up your box without strain.
gmx genconf -nbox 2 2 1 may help you. Note you'll have to redo the
topology.

Cheers,

On Thu, Nov 26, 2015 at 11:11 AM, Golnaz Roudsari <golnaz.chem at gmail.com> wrote:
> Dear users
> I got this error in my mdrun There is no domain decomposition for 4 nodes
> that are compatible with the given box and a minimum cell size of 7.1147
> nm. my system contains graphene and surfactants. In last box I put graphene
> in the middle of my box and the graphene was npbc and the mdrun went well,
> then I put a pbc graphene and the x and y dimension box fixed to match the
> size of graphene sheet. but in energy minimization step. I get this error!
> Can I put the x, y dimension of my box larger than pbc graphene?
> thank you for any suggestion
> Golnaz
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-- 
Elton Carvalho