According to your MD parameters, your system should attain T=300K at the 300th nanosecond.
Since you have run only for 500000 * 0.002 ps = 1ns, you got T=1K, since temperature elevates linearly, based on your setup. Dr. Vitaly Chaban On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger <hoe...@gmail.com> wrote: > Hi, > > I have a system setup (minimized etc.) and wanted to heat this system > gradually with simulated annealing. I set up the mdp file as you can see > below (simulated annealing part is marked bold). But when the heating is > finished, the log file tells me that the temperature of the system is only > 1K (see below). > > Can someone tell me what I am doing wrong? > > > Best, > Marc > > ;************ PREPROCESSING ********************************************* > ;include = > ;define = > ;************ RUN CONTROL *********************************************** > dt = 0.002 ; timestep, 2 fs > integrator = md ; leap-frog integrator > nsteps = 500000 ; 2 * 500000 = 1000 ps > tinit = 0 ; starting time, ps > init_step = 0 ; starting step > comm-mode = linear ; remove COM translation > nstcomm = 10 ; freq steps comm-mode > comm-grps = system ; groups COM removal ; protein > nstcalcenergy = -1 ; freq calc ener; default = nstlist > ;************ DYNAMICS ************************************************** > ;### Initial velocity assignment > gen_vel = yes ; assign velocities from Maxwell > distribution > gen_temp = 300 ; temperature for Maxwell > distribution > gen_seed = -1 ; random generator seed; -1 from > job ID > ;************ OUTPUT CONTROL ******************************************** > ;### xtc > nstxtcout = 2500 ; .xtc freq write coor > xtc-precision = 1000 ; .xtc precision > xtc_grps = system ; .xtc saved groups > ;### trr > nstxout = 500000 ; .trr freq write coor > nstvout = 500000 ; .trr freq write vel > nstfout = 0 ; .trr freq write forces > ;### log > nstlog = 2500 ; .log freq write ener > ;### edr > nstenergy = 2500 ; .edr freq write ener; = > i*nstcalcenergy > energygrps = protein non-protein ; .edr saved groups > ;************ NON-BONDED INTERACTIONS *********************************** > ns_type = grid ; search neighbor grid cells > nstlist = 10 ; freq update NB list > > vdwtype = switch ; switching function for VdW > coulombtype = PME ; PME for long-range electrostatics > rvdw_switch = 0.9 ; switching dist VdW > rvdw = 1.0 ; cutoff VdW > rcoulomb = 1.2 ; cutoff elec > rlist = 1.2 ; cutoff NB list; must = rcoulomb > when PME > > epsilon-r = 1 ; dielectric const > DispCorr = EnerPres ; Long-range VdW dispersion > correction > > ;### PME & Ewald > ewald_rtol = 1.0e-5 ; direct space tolerance; > 1.0e-6/2.2e-5 > fourierspacing = 0.12 ; max grid spacing for FFT > pme_order = 6 ; interpolation order; depends on > cutoff > ewald_geometry = 3d ; Ewald in 3d > epsilon_surface = 0 ; dipole correction for 3d Ewald > optimize_fft = yes ; start-up FFT grid optimization > ;************ BOUNDARY CONTROL ****************************************** > pbc = xyz ; 3-D PBC > ;************ CONSTRAINTS CONTROL *************************************** > constraints = all-bonds ; all bonds (even heavy atom-H > bonds) constrained > continuation = no ; constraints applied to initial > conf > constraint_algorithm = lincs ; holonomic constraints > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > lincs_warnangle = 30 ; max allowed bond angle before > warning > ;************ TEMPERATURE CONTROL *************************************** > tcoupl = nose-hoover ; Nose-Hoover T-coupling; v-rescale > tc-grps = system ; two coupling groups - more > accurate > tau_t = 0.6 ; coupling time constant at equil, > in ps > ref_t = 300 ; reference temperature, one for > each group, in K > ;************ PRESSURE CONTROL ****************************************** > pcoupl = Parrinello-Rahman ; Pressure coupling on in > NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 1.0 ; coupling time constant at equil, > in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5 ; isothermal compressibility of > water at 1 atm, bar^-1 > ;************ SIMULATED ANNEALING > ****************************************** > *annealing = single ; type of annealing (single > sequence of annealing points)* > *annealing_npoints = 2 ; # of temperature points* > *annealing_time = 0 300000 ; time window in which temperature > shall be increased* > *annealing_temp = 0 300 ; temperature at timepoints* > > > LOG-FILE: > Writing checkpoint, step 500000 at Thu Jun 6 21:23:55 2013 > > > *Current ref_t for group System: 1.0* > Energies (kJ/mol) > U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 > 8.64012e+03 5.98740e+03 4.75546e+02 -1.72734e+03 4.25420e+03 > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > 4.78689e+04 1.75858e+05 -5.83865e+03 -1.21361e+06 -1.12292e+05 > Position Rest. Potential Kinetic En. Total Energy Temperature > 7.52594e+00 -1.09037e+06 1.35115e+05 -9.55257e+05 2.17729e+02 > Pres. DC (bar) Pressure (bar) Constr. rmsd > -1.35977e+02 1.38325e+02 2.75899e-05 > -- > 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/Support/Mailing_Lists/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? 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