Dear Gromacs users, I am working with membrane proteins. The system contains CaCl2 ions and I build the system with calcium ions on one side of the membrane (here, upper layer) and chloride ions distributed on both side of the membrane, in order to maintain the physiological condition. Unfortunately, after the very first minimization, when I visualize the gro file in VMD I have noticed that the calcium ions entered the opposite side of the membrane (ie, lower layer) and subsequently get distributed in the lower layer during the equilibration process. Though I have tried with varying Z-dimension values of the box size, the same has been noticed when visualizing the output gro file with VMD.
Please help me to figure out what is wrong with my simulation box. Many thanks Anu -- 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.