[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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