[gmx-users] Neighbor searching artifacts in permittivity when using shift

Julian Michalowsky j.michalowsky at gmail.com
Wed Nov 23 13:19:23 CET 2016


I am using gromacs 5.1.0 with the Martini force field. When trying to
reproduce some data regarding the 2010 Martini polarizable water model, I
noticed that it is affected by the values of rlist and nstlist. In the
reference work, the following parameters are used:




Along with this, Berendsen weak coupling schemes were used. I myself on the
other hand use the v-rescale thermostat and parrinello-rahman barostat, but
I can reproduce the reference data if I use the respective values for rlist
and nstlist.

What I did: In one set of simulations, I varied rlist=1.20, 1.22,...,1.40
and kept nstlist=1. In another set, I set rlist=1.20 and varied
nstlist=1,2,...,10. For each simulation, I calculated the permittivity
using gmx dipoles. Simulations are each 100ns NPT production runs and
sufficiently equilibrated; boxes contain 2797 polarizable water beads (and
nothing else).

What I expected: No variation in the first set of simulations, as the
smallest value for rlist is still >= the largest interaction cutoff, and I
update the neighbor lists every time step (nstlist=1). I expect some
variations when changing the value of nstlist, though, and keeping

What I found: Variations of the measured permittivity in both simulation
sets (monotonous trends). The permittivity was even stronger influenced by
variations of rlist.

What I am wondering about is why rlist influences the data, despite rlist
>= rvdw and nstlist=1, and if this should be the case. If so, there is some
conceptual thing I don't quite understand about how the group neighbor list
implementation in Gromacs works, and I kindly ask for an explanation. If
not, then I guess there is something going on that shouldn't be, or I made
a different mistake. In any case, I require some assistance on this one.

On a sidenote: I know that the 'shift' statement is deprecated, but it
worked for me using different Gromacs versions, including 5.0.5 and 5.1.0.
Trying to use the potential modifier force-switch instead results in
immediate system crashes after minimization, so they are probably not 100%
interchangable (which is what I thought they were supposed to be).

Thanks a lot in advance for your help.

Kind Regards,
Julian Michalowsky

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