Hi there, We are doing simulation in which we are interested in studying Energies, Enthalpies, etc. changes in systems with increasingly water shells around a protein. In this sense, we first extract bulk waters in order to leave the mentioned water shells with a defined radius around the protein. Then we do a rerun in order to recalculate the system energies, but my doubt here is: what exactly to do with PBC in the .mdp file? My doubts here come up because the system now (protein + water shell) is not a geometric box like a dodecahedron or a cubic box, and I am afraid about whether the energies I am obtaining are totally wrong. Do you think it will be better here not to use PBC or you think there is no matter in doing the rerun keeping PBC on? I guess that keeping PBC on, there will be some empty space between each side box (the space left by water removed), so I feel it could be important ...
Thank you very much. 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.
