Hi Justin, I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right?
Thanks, Lan On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul <[email protected]> wrote: > > > Lan Hua wrote: > >> 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 <[email protected]<mailto: >> [email protected]>> 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. >> >> > > OK, as long as you've got a reason... > > > >> >> 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. >> >> > > I just mean the repeated, separate energy minimizations. I guess there's > no harm in it, but generally I find that minimizing the protein in vacuo, > then with and without restraints in solvent, etc. is unnecessary. I'd > suggest just building the system (solvent and all), and minimizing the whole > thing (without restraints). I don't think you stand to gain anything with > your procedure. > > > >> >> 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 >> > > At least for the thermostat, but yes, probably it can't hurt to use weak > coupling for both temperature and pressure. > > > question. If I choose constraints = hbonds instead of constraints = >> all-bonds in NPT simulation, what will happen? >> >> > You constrain heavy atom-H bonds instead of all bonds. Using fewer > constraints may or may not affect the magnitude of the time step you can > use, but generally X-H bonds are the highest frequency and thus are the > least stable with long time steps. > > -Justin > > >> 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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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. Use the www >> interface or send it to [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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/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/mailing_lists/users.php >
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