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

Peter Kroon p.c.kroon at rug.nl
Tue Nov 29 11:30:57 CET 2016

Hi Julian,

unfortunately I can't answer you question regarding the neighbour search
algorithm. However, it should be noted that there are alternative mdp
parameters available for Martini using the Verlet cutoff-scheme, made
specifically for gromacs 5. Would you be willing to try those? You can
find them here:
Particularly the new-rf settings should be applicable.



On 23-11-16 13:19, Julian Michalowsky wrote:
> Hi,
> 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:
> cutoff-scheme=group
> nstlist=5
> rlist=1.2
> vdwtype=shift
> rvdw=1.2
> rvdw-switch=0.9
> coulombtype=shift
> rcoulomb=1.2
> rcoulomb-switch=0.0
> 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
> rlist=rvdw=rcoulomb.
> 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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