Hi Shine, I have a query, before packing the lipids around the protein and ligand did you restrain the whole system i.e protein and ligand and in the em.mdp file is this vat you specified "define = -DSTRONG_POSRES".... Please let me know.
Thanks in advance Swati. On Tue, Apr 9, 2013 at 4:50 PM, Anirban <reach.anirban.gh...@gmail.com>wrote: > After NVT, usually the lipid bilayer move away from each other creating > some voids, which occurs due to absence of pressure coupling. But its not a > problem. You can go ahead and carry out NPT and see that bilayer has > settled to normal position. > > -Anirban > > > On Tue, Apr 9, 2013 at 3:04 PM, sdshine <sdsh...@gmail.com> wrote: > > > Gromacs users, > > > > My complex heterogenous system has DPPC+ Protein+ligand. I have packed > > lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 > > got > > after 24th iteration) followed by adding solvent and neutralize the > system > > by adding CL35 & NA 39, since my system has -3.999 non zero total charge. > > Then the minimized system has the energy -2.8989 with Max force= 9.58 > > converged normally in step 464 step. > > > > I used lipid constraints in the file "DPOSRES_LIPID.itp" before NVT > > > > ; position restraint file for DPPC P8 > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 8 1 0 0 1000 > > ------------------------------------------------------- > > > > My topology has the last part... > > ---- > > ------- > > ; Include Position restraint file > > #ifdef POSRES > > #include "posre.itp" > > #endif > > > > ; Include lig topology > > #include "lig.itp" > > > > ; Strong position restraints for InflateGRO > > #ifdef STRONG_POSRES > > #include "DSTRONG_POSRES_B.itp" > > #endif > > > > ; Include DPPC topology > > #include "dppc.itp" > > > > ;strong position restraints for DPPC > > #ifdef POSRES_LIPID > > #include "DPOSRES_LIPID.itp" > > #endif > > > > ; Include water topology > > #include "spc.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcx fcy fcz > > 1 1 1000 1000 1000 > > #endif > > > > ; Include generic topology for ions > > #include "ions.itp" > > > > [ system ] > > ; Name > > complex protein in water > > > > [ molecules ] > > ; Compound #mols > > Protein_G 1 > > Lig 1 > > DPPC 125 > > SOL 3199 > > CL 35 > > NA 39 > > ----------------------------------- > > > > There is no grompp error and no problem till NVT, after this > > equillibration, > > half of the DPPC along with SOL is no showing in VMD. Could any > suggestions > > on this behavior. > > > > Thanks in advance > > > > -Shine > > > > > > > > > > > > > > -- > > View this message in context: > > > http://gromacs.5086.x6.nabble.com/Lipid-membrane-partially-broken-and-create-huge-voids-after-NVT-tp5007128.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
