[gmx-users] System does not heat up to 300K.
Dr. Vitaly Chaban
vvchaban at gmail.com
Tue Jun 11 20:12:53 CEST 2013
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 <hoembi at 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
> --
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