<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>The comment from Justin and your answer to it were pretty convincing.<div>I think the problem is solved :)).</div><div><br></div><div>Tom is correct to get T with g_energy on a simulation that ran with one</div><div>Tcoup, you need to rerun the trajectory (trr) with a tpr in which you </div><div>define two Tcoup. This should give you T for each group.</div><div><br></div><div>XAvier.</div><div><br><div><br><div><div>On Oct 29, 2009, at 11:11 PM, Michael Lerner wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div class="im"><br> On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> I calculated temperatures with<br> <br> g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5<br> </blockquote></div> I did not know you could get the temperature throught g_traj ... the -ot option is the one<br> giving you the temperature?<br> <br></blockquote><div><br>Yes.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Do you get the same temperature difference with g_energy? Or may be the info is not<br> in there? May be you could rerun you trajectory using a new tpr where you define two<br> different temp coupling groups. And see if you observe the same temperature given by<br> g_energy.<br></blockquote><div><br>It's possible that I'm doing something wrong, but I couldn't convince g_energy to give me the temperature of different groups when I used a single thermostat for the entire system. If I use two temperature coupling groups, I get the expected results.<br> <br>As Justin pointed out, it looks like the error was mine for not understanding the details of g_traj. When I manually correct for the degrees of freedom, I get temperatures for Protein/Sol that are close enough to each other (i.e. within a couple of standard deviations).<br> <br>Thanks,<br><br>-Michael<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"> <br> Thanks,<br> <br> -Michael<br> <br> ------ begin md2.mdp ------<br> <br> ; RUN CONTROL PARAMETERS =<br> integrator = md<br> ; start time and timestep in ps =<br> tinit = 0.0<br> dt = 0.020<br> nsteps = 25500000<br> ; mode for center of mass motion removal<br> comm-mode = linear<br> ; number of steps for center of mass motion removal<br> nstcomm = 1<br> ; group(s) for center of mass motion removal<br> comm-grps = System<br> <br> <br> ; OUTPUT CONTROL OPTIONS =<br> ; Output frequency for coords (x), velocities (v) and forces (f) =<br> nstxout = 50000<br> nstvout = 50000<br> nstfout = 0<br> ; Output frequency for energies to log file and energy file =<br> nstlog = 2500<br> nstenergy = 2500<br> ; Output frequency and precision for xtc file =<br> nstxtcout = 2500<br> xtc_precision = 100<br> ; This selects the subset of atoms for the xtc file. You can =<br> ; select multiple groups. By default all atoms will be written. =<br> xtc-grps =<br> ; Selection of energy groups =<br> energygrps = System Protein W WF<br> <br> ; NEIGHBORSEARCHING PARAMETERS =<br> ; nblist update frequency =<br> nstlist = 5<br> ; ns algorithm (simple or grid) =<br> ns_type = grid<br> ; Periodic boundary conditions: xyz or none =<br> pbc = xyz<br> ; nblist cut-off =<br> rlist = 1.2<br> <br> ; OPTIONS FOR ELECTROSTATICS AND VDW =<br> ; Method for doing electrostatics =<br> coulombtype = Shift<br> rcoulomb_switch = 0.0<br> rcoulomb = 1.2<br> ; Dielectric constant (DC) for cut-off or DC of reaction field =<br> epsilon_r = 15<br> ; Method for doing Van der Waals =<br> vdw_type = Shift<br> ; cut-off lengths =<br> rvdw_switch = 0.9<br> rvdw = 1.2<br> ; Apply long range dispersion corrections for Energy and Pressure =<br> DispCorr = No<br> ; Spacing for the PME/PPPM FFT grid =<br> fourierspacing = 0.12<br> ; FFT grid size, when a value is 0 fourierspacing will be used =<br> fourier_nx = 10<br> fourier_ny = 10<br> fourier_nz = 10<br> ; EWALD/PME/PPPM parameters =<br> pme_order = 4<br> ewald_rtol = 1e-05<br> epsilon_surface = 0<br> optimize_fft = no<br> <br> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =<br> ; Temperature coupling =<br> tcoupl = Nose-Hoover<br> ; Groups to couple separately =<br> tc-grps = System<br> ; Time constant (ps) and reference temperature (K) =<br> tau_t = 2<br> ref_t = 323<br> ; Pressure coupling =<br> Pcoupl = Parrinello-Rahman<br> Pcoupltype = isotropic<br> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =<br> tau_p = 5<br> compressibility = 5e-5<br> ref_p = 1.0<br> <br> ; SIMULATED ANNEALING CONTROL =<br> annealing = no<br> <br> ; GENERATE VELOCITIES FOR STARTUP RUN =<br> continuation = yes<br> gen_vel = no<br> ;gen_temp = 323<br> ;gen_seed = 473529<br> <br> ; OPTIONS FOR BONDS =<br> constraints = none<br> ; Type of constraint algorithm =<br> constraint_algorithm = Lincs<br> ; Relative tolerance of shake =<br> shake_tol = 0.0001<br> ; Highest order in the expansion of the constraint coupling matrix =<br> lincs_order = 4<br> ; Lincs will write a warning to the stderr if in one step a bond =<br> ; rotates over more degrees than =<br> lincs_warnangle = 30<br> ; Convert harmonic bonds to morse potentials =<br> morse = no<br> <br> ; NMR refinement stuff =<br> ; Distance restraints type: No, Simple or Ensemble =<br> disre = No<br> ; Force weighting of pairs in one distance restraint: Equal or Conservative =<br> disre_weighting = Equal<br> ; Use sqrt of the time averaged times the instantaneous violation =<br> disre_mixed = no<br> disre_fc = 1000<br> disre_tau = 1.25<br> ; Output frequency for pair distances to energy file =<br> nstdisreout = 100<br> ------- end md2.mdp -------<br> <br> <br> <br> -- <br> Michael Lerner, Ph.D.<br> IRTA Postdoctoral Fellow<br> Laboratory of Computational Biology NIH/NHLBI<br> 5635 Fishers Lane, Room T909, MSC 9314<br> Rockville, MD 20852 (UPS/FedEx/Reality)<br> Bethesda MD 20892-9314 (USPS)<br></div></div> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote> <br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote></div><br><br clear="all"><br>-- <br>Michael Lerner, Ph.D.<br>IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>Rockville, MD 20852 (UPS/FedEx/Reality)<br> Bethesda MD 20892-9314 (USPS)<br> _______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></div></body></html>