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
