[gmx-users] System does not heat up to 300K.
Marc Hoemberger
hoemberg at brandeis.edu
Tue Jun 11 20:18:01 CEST 2013
Thanks, I must have confused the units for the simulated annealing
parameters.
On Tue, Jun 11, 2013 at 2:12 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>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 <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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