Thanks Mark for your replay. About the part where you say...
>The problem comes when one side of your shell can see >the other across the gap within the cutoff, and you're still thinking of it >as an isolated single shell ...yes, I agree with you that one must be aware about this issue. But about the other aspect you pointed out: >or if you're using PME, so that everything >sees everything at long range ...I'm not so clear. The point is we've used PME both in the original simulations and in the 'rerun' ones (the .mdp files are almost idem). Then, what should we do here to avoid this problem? ...maybe to turn off the PME long-range electrostatics only in the rerun step? If so, wouldn't that importantly change results in terms of Energy only by the effect of changing the electrostatic treatment? Another solution? ...maybe setting up a different electrostatics from the begining (the same both in the original simulations and in the rerun ones)? What's treatment we could use to get the longe-range electrostatics turned off without loosing so much accuracy in terms of Energy? ...'cut-off', 'PME-Switch' maybe? ... or a coulomb-modifier such as Potential-shift-Verlet? Any suggestion there, please? Thanks a lot. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-February/111037.html Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and Physics of Complex Systems (BIFI) Mariano Esquillor, Edificio I + D - 50018 Zaragoza (Spain) -- 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.
