The .mdp file parameter for electric field is as follows. E_z = 1 -0.7 1 ; electric field
I want to stop the movement of bi-layer along the z axis as the hypothesis is to check whether a super charge protein can dislocate the DPPC bi-layer under an electric field. Correction, the electric field applied is 0.7V/nm On Tue, Nov 21, 2017 at 9:08 AM, Alex <nedoma...@gmail.com> wrote: > I've never worked with CG models, but I assume that the lipid structure is > well-represented and electrically neutral. That said, uncompensated > momentum in all MD simulations can arise when a high driving field is > applied suddenly instead of a ramp. When you say that your field is > -0.7mV/nm, > does this mean that it's something like "E-z = 1 -0.0007 > 0.0 > " in your mdp file? The units are V/nm, not mV/nm. > > Alex > > On Mon, Nov 20, 2017 at 6:15 PM, Sithara Perera < > sithara.perera1...@gmail.com> wrote: > > > Yes. The system was stable and simulations showed that the bi-layer is > > before applying an electric field. > > > > On Tue, Nov 21, 2017 at 1:59 AM, Alex <nedoma...@gmail.com> wrote: > > > > > Do you precede your production simulation with a relaxation run without > > an > > > electric field? > > > > > > Alex > > > > > > > > > > > > On 11/20/2017 12:16 PM, Sithara Perera wrote: > > > > > >> Dear gmx-users, > > >> > > >> I'm doing molecular dynamic simulations of protein interaction with > > lipid > > >> bi layers using CGmartini force fields under an electric field. > > >> > > >> But when I apply the electric field and simulated for 50 ns under > > >> -0.7mV/nm, the bi layer moves in the electric field and then > eventually > > >> reaches the bottom of simulation box. So it is not possible to see the > > >> protein interaction with the bi layer. I tried applying position > > restrains > > >> on z axis, but then the box dimensions started to change > > >> > > >> The bi layer a 512DPPC bi layer. > > >> What can I do to fix this?? > > >> > > >> > > >> > > >> --------- > > >> Sithara Perera > > >> USJP > > >> > > > > > > -- > > > 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. > -- 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.