[gmx-users] Nstlist and constrain simulations

Michail Palaiokostas Avramidis m.palaiokostas at qmul.ac.uk
Mon Feb 1 18:42:13 CET 2016

Dear GMX users,

I would like to ask about your opinion on the size of the neighbour list (nstlist).

I am running constraint simulations of a permeant along a lipid bilayer. In the initial setup the system runs on NPT and nstlist 10 (which GROMACS changes to 40 automatically). With this setup my simulation is very fast but always crashes at various points with the same way always. Initially it gives some LINCS warnings and then it gives an error that a particle "communicated to PME rank 2 are more than 2/3 times the cut-off out of the domain decomposition cell".

When I see the last pdb steps before crash, sometimes there seem to be overlaps between the permeants and the lipids and then system explosions and PBChaos. Other times it is not so dramatic.

So the question is, should I be conservative with the nstlist? When I run NPT simulations and change the nstlist to 1, the system does not fail. Alternatively, if I change to NVT and nstlist to 10, again the system runs successfully. But NVT and 40 crashes.

Since GROMACS was doing the nstlist update automatically, I thought it was a "safe" option. Based on the above,however, I believe that since the simulation runs with constraints, the system is more sensitive and thus the nstlist should be smaller. Can anyone validate that my hypothesis is correct?

Thanks in advance.

Kind Regards,


Michail (Michalis) Palaiokostas
PhD Student
School of Engineering and Materials Science
Queen Mary University of London

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