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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.