Hi Justin, Thank you so much for your quick reply and good suggestions. The following is my answer.
On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Lan Hua wrote: > >> Hi All, >> >> I understand that the error of segmentation fault may come from many >> reasons, but I just couldn't figure out the reason of this error in my >> simulations. I want to run md simulations with explicit water for 20 >> structures of one domain (residue 77-148) of calmodulin (PDB 1CFC). These >> 20 starting structures are from one REMD simulation in implicit water. The >> following is what I did to run simulations for these 20 structures. I used >> gromacs version 3.1.4 with ffamber ports. The force field is amber03 and >> water model is TIP3P. >> >> > Do you have any particular reason for using software that is eight years > old? You will get a massive performance upgrade with 4.0.7, as well as the > ability to use multiple processors per replica. In versions prior to 4.0, > you can only use one processor per REMD replica. > > The reason that I am using gromacs 3.1.4 is to prepare some input files for simulations at fold...@home in which version 3.1.4 is recommended. > > 1. get rid of the steric clash in the starting structure >> > > What do you mean? Energy minimization? How did you did do this prior to > step 2 (generating a topology)? > > I used the "protein preparation wizard" which is implemented in maestro package to do this. Actually in this wizard, energy minimization is performed on protein. > > 2. after doing pdb2gmx, then minimze the protein >> 3, use "-bt dodecahedron -d 0.9 -c" in the command line of editconf >> 4, after doing genbox, first minimize the water with protein rigid and >> then minimize the whole system >> > > A lot of these steps are redundant and probably unnecessary. Some tips: > > http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation > > Thanks for the tips. I went to the link, but I am still a little bit confused about which steps are unnecessary. You mean step 7 and step 8? I did this in case simulations at f...@h would be crashed. > > 5, run md simulation with position restraint for protein heavy atoms >> with nose-hoover thermostat for 20ps >> 6, run NPT simulations with nose-hoover thermostat and >> Parrinello-Rahman thermostat for 500ps >> 7, run NVT simulation for another 100ps >> 8, then energy minimze the whole system again. >> >> Every time, there are always "segmentation fault" in step 6 for some >> starting structures which could be different in every try. I checked the >> energy, volume, pressure, temperature, etc for the trajectories which are >> crashed because of segmentation fault, but nothing was wrong. I roughly >> checked the trajectory which looks fine. I also couldn't find any useful >> information from the log file, which looks like the following: >> >> > Using weak coupling (i.e. Berendsen) coupling is generally recommended for > initial equilibration. If a system is far from equilibrium (as it likely > will be after adding patterned blocks of water with genbox), the N-H > thermostat can allow for wild changes in the temperature of the system, > leading to a collapse. > > Your temperature coupling groups are also inappropriate: > > Tcoupl = nose-hoover > tc_grps = Protein SOL Na > tau_t = 0.1 0.1 0.1 > > Never couple solvent and ions separately; it can lead to instability: > > http://www.gromacs.org/Documentation/Terminology/Thermostats > These are good suggestions. Thanks. So use Berendsen coupling for both temperature and pressure coupling for initial equilibration, for example position restrained NVT followed by NPT, right? I have another question. If I choose constraints = hbonds instead of constraints = all-bonds in NPT simulation, what will happen? Best, Lan > > -Justin > > > Step Time Lambda Annealing >> 180000 360.00003 0.00000 1.00000 >> >> Rel. Constraint Deviation: Max between atoms RMS >> Before LINCS 0.045887 47 48 0.004584 >> After LINCS 0.000020 752 755 0.000003 >> >> Energies (kJ/mol) >> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 >> 2.08335e+03 1.59908e+02 2.95659e+03 1.17109e+03 1.27711e+04 >> LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential >> 4.10779e+04 -1.37728e+03 -2.89916e+05 -5.82443e+04 -2.89318e+05 >> Kinetic En. Total Energy Temperature Pressure (bar) >> 5.25584e+04 -2.36759e+05 2.96920e+02 -1.07683e+02 >> >> Step Time Lambda Annealing >> 185000 370.00003 0.00000 1.00000 >> >> Rel. Constraint Deviation: Max between atoms RMS >> Before LINCS 0.052014 70 71 0.005149 >> After LINCS 0.000011 214 215 0.000002 >> >> Energies (kJ/mol) >> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 >> 2.33684e+03 1.42695e+02 2.91169e+03 1.18452e+03 1.28507e+04 >> LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential >> 4.06987e+04 -1.37332e+03 -2.88889e+05 -5.83180e+04 -2.88455e+05 >> Kinetic En. Total Energy Temperature >> >> The *.mdp files are also attached. Any help will be highly appreciated. >> Thank you. >> >> >> Best, >> Lan >> >> > -- > ======================================== > > 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 gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. 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