Thanks, I must have confused the units for the simulated annealing parameters.
On Tue, Jun 11, 2013 at 2:12 PM, Dr. Vitaly Chaban <[email protected]>wrote: > 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 <[email protected]> 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 [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
