Dear Justin Thanks greatly for your suggestions. I will try a new series of EMs and NPT equilibrations to find whether it will be of effect.
Li 2011/5/14 Justin A. Lemkul <[email protected]> > > > li lv wrote: > >> 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. >> >> > But do you maintain position restraints? Restraints during minimization > serve little use, and they actually are probably preventing some necessary > structural changes from happening. I'd suspect that's the reason for your > instability - you're not minimizing as well as your system requires. > > I would also say that there is no point in using both freezegrps and > position restraints during equilibration, especially NPT, where freezegrps > actually interfere with proper coordinate scaling. I would suggest you > simply use position restraints. > > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
