Re: [gmx-users] Lipid membrane partially broken and create huge voids after NVT
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.comwrote: 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 fcxfcyfcz 81 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 fcxfcyfcz 11 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 listgmx-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 listgmx-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 listgmx-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] Lipid membrane partially broken and create huge voids after NVT
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 fcxfcyfcz 81 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 fcxfcyfcz 11 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 listgmx-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
Re: [gmx-users] Lipid membrane partially broken and create huge voids after NVT
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 fcxfcyfcz 81 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 fcxfcyfcz 11 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 listgmx-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 listgmx-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
