Dear Justin
Thanks for your reply. Generally I conduct the simulation following the tutorial on your website. The system contains an integrin alpha2b/beta3 transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer and solvated in water. The initial membrane-protein system is built with INFLATEGRO. Here is the topology file of the system (not completed): “ ; Include forcefield parameters #include "ffG53a6_lipid.itp" ; Include chain topologies #include "topol_A.itp" ; Include Position restraint file #ifdef POSRES #include "posre_A.itp" #endif #include "topol_B.itp" ; Include Position restraint file #ifdef POSRES #include "posre_B.itp" #endif ; Include DPPC chain topology #include "dppc.itp" ; 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 Protein in water [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 DPPC 124 SOL 17185 NA+ 2 ” For the details of energy minimization, here is one of the mdp files for energy minimization: “ define = -DPOSRES integrator = cg emtol = 500.0 emstep = 0.01 nstcgsteep = 100 nsteps = 50000 nstlist = 1 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz freezegrps = Protein-H freezedim = Y Y Y ” As you may notice, I froze the heavy atoms of the protein during the first energy minimization and then in the following the EMs the frozen group was MainChain, C-alpha and none in order. The system finally reached Fmax < 500. The similar method was employed in the NPT equilibration and here is one of the mdp files: “ title = NPT Equilibration define = -DPOSRES integrator = md nsteps = 100000 dt = 0.0005 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 continuation = yes constraint_algorithm = lincs constraints = none lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps = Protein DPPC SOL_NA+ tau_t = 0.5 0.5 0.5 ref_t = 323 323 323 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 2.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no gen_temp = 323 gen_seed = -1 nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_NA+ freezegrps = Protein-H freezedim = Y Y Y ” Hope those information may help you and others understand my problem. Li
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