Hi, It looks like the the problem is the asymmetry in ion distribution. I have seen from the literature that such ion asymmetry can be maintain by implementing slab geometry. Can anybody provide me some information of how to build vacuum slab above and below the membrane ( ie in Z direction). What all modification I should make in mdp input file to take care of the slab geometry?
Many thanks in advance Anu On Tue, Jul 14, 2015 at 3:57 PM, anu chandra <anu80...@gmail.com> wrote: > Thanks for the reply Mark. Yes, its a periodic box. Below is the input mdp > I have used for minimization. > > define = -DREST_ON -DSTEP6_0 > integrator = steep > emtol = 1000.0 > nsteps = 5000 > nstlist = 10 > cutoff-scheme = Verlet > rlist = 1.2 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.2 > coulombtype = pme > rcoulomb = 1.2 > ; > constraints = h-bonds > constraint_algorithm = LINCS > > ************************************************************** > > Please find attached the snapshot of the system before (initial.png) and > after minimization (min1.png). Green is the calcium ions and blue is the > chloride ions. All I have done is adding calcium ions to one side of the > membrane. It looks to me like calcium ions enetering from the opposite side > of the box ( ie from its image box). Hope I am taking care of the periodic > condition. Please have a look and help me to figure out the problem. > > On Tue, Jul 14, 2015 at 11:47 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> It's a periodic box, right? There is only one water region. You can't get >> steady-state non-equilibrium ion distribution without forcing it, e.g. >> https://www.mpibpc.mpg.de/grubmueller/compel >> >> Mark >> >> On Tue, Jul 14, 2015 at 12:42 PM anu chandra <anu80...@gmail.com> wrote: >> >> > 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. >> > >> -- >> 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. >> > > -- 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.