On Thu, Oct 29, 2009 at 5:38 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > I see you are using "constraints = none," but are there any constraints > defined in the topology? If so, as noted in g_traj -h: > > "Option -ot plots the temperature of each group, provided velocities are > present in the trajectory file. No corrections are made for constrained > degrees of freedom! This implies -com." > > So you will get an inherently incorrect answer when using g_traj, if there > are any constraints. > > Oops! I actually had read some previous messages about that, but I got confused and thought the problem was with g_energy, not g_traj. I'm not particularly familiar with the GROMACS source code, but gmx_traj.c has this function: static real temp(rvec v[],real mass[],int isize,atom_id index[]) { real ekin2=0; int i,j; for(i=0; i<isize; i++) { j = index[i]; ekin2 += mass[j]*norm2(v[j]); } return ekin2/(3*isize*BOLTZ); } so it looks like g_traj is just assuming that there are 3*N degrees of freedom. My protein topology file has 304 particles and 83 lines in the constraints section, so I think the correction should be 295.3496*((3*304)/(3*304 - 83)) = 324.9202 for my protein vs. 322.9525 for the W's and 322.9279 for the WF's. So, they're still a little off, but doing some block averaging and looking at standard errors, it's well within the acceptable range. Thanks, -Michael > -Justin > > Thanks, >> >> -Michael >> >> ------ begin md2.mdp ------ >> >> ; RUN CONTROL PARAMETERS = >> integrator = md >> ; start time and timestep in ps = >> tinit = 0.0 >> dt = 0.020 >> nsteps = 25500000 >> ; mode for center of mass motion removal >> comm-mode = linear >> ; number of steps for center of mass motion removal >> nstcomm = 1 >> ; group(s) for center of mass motion removal >> comm-grps = System >> >> >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 50000 >> nstvout = 50000 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file = >> nstlog = 2500 >> nstenergy = 2500 >> ; Output frequency and precision for xtc file = >> nstxtcout = 2500 >> xtc_precision = 100 >> ; This selects the subset of atoms for the xtc file. You can = >> ; select multiple groups. By default all atoms will be written. = >> xtc-grps = >> ; Selection of energy groups = >> energygrps = System Protein W WF >> >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist = 5 >> ; ns algorithm (simple or grid) = >> ns_type = grid >> ; Periodic boundary conditions: xyz or none = >> pbc = xyz >> ; nblist cut-off = >> rlist = 1.2 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW = >> ; Method for doing electrostatics = >> coulombtype = Shift >> rcoulomb_switch = 0.0 >> rcoulomb = 1.2 >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon_r = 15 >> ; Method for doing Van der Waals = >> vdw_type = Shift >> ; cut-off lengths = >> rvdw_switch = 0.9 >> rvdw = 1.2 >> ; Apply long range dispersion corrections for Energy and Pressure = >> DispCorr = No >> ; Spacing for the PME/PPPM FFT grid = >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 10 >> fourier_ny = 10 >> fourier_nz = 10 >> ; EWALD/PME/PPPM parameters = >> pme_order = 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS = >> ; Temperature coupling = >> tcoupl = Nose-Hoover >> ; Groups to couple separately = >> tc-grps = System >> ; Time constant (ps) and reference temperature (K) = >> tau_t = 2 >> ref_t = 323 >> ; Pressure coupling = >> Pcoupl = Parrinello-Rahman >> Pcoupltype = isotropic >> ; Time constant (ps), compressibility (1/bar) and reference P (bar) = >> tau_p = 5 >> compressibility = 5e-5 >> ref_p = 1.0 >> >> ; SIMULATED ANNEALING CONTROL = >> annealing = no >> >> ; GENERATE VELOCITIES FOR STARTUP RUN = >> continuation = yes >> gen_vel = no >> ;gen_temp = 323 >> ;gen_seed = 473529 >> >> ; OPTIONS FOR BONDS = >> constraints = none >> ; Type of constraint algorithm = >> constraint_algorithm = Lincs >> ; Relative tolerance of shake = >> shake_tol = 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs_order = 4 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs_warnangle = 30 >> ; Convert harmonic bonds to morse potentials = >> morse = no >> >> ; NMR refinement stuff = >> ; Distance restraints type: No, Simple or Ensemble = >> disre = No >> ; Force weighting of pairs in one distance restraint: Equal or >> Conservative = >> disre_weighting = Equal >> ; Use sqrt of the time averaged times the instantaneous violation = >> disre_mixed = no >> disre_fc = 1000 >> disre_tau = 1.25 >> ; Output frequency for pair distances to energy file = >> nstdisreout = 100 >> ------- end md2.mdp ------- >> >> >> >> -- >> Michael Lerner, Ph.D. >> IRTA Postdoctoral Fellow >> Laboratory of Computational Biology NIH/NHLBI >> 5635 Fishers Lane, Room T909, MSC 9314 >> Rockville, MD 20852 (UPS/FedEx/Reality) >> Bethesda MD 20892-9314 (USPS) >> >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> 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. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS)
_______________________________________________ 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php