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
