[gmx-users] simmulated annealing

[Mark Abraham]

On 13/08/2012 4:09 AM, tarak karmakar wrote:
> Dear All,
>
> I did the simmulated annealing for a protein where I wanted to
> increase the temperature from 0 K to 300 K after 300 ps. But after the
> simulation run I see the temp got increased up to 400 K and so.
> So can anyone tell me whether I am doing any mistake ?

Don't know, you gave us the .mdp file for the run you thought worked, 
and not the one for the run you think might have a problem.

> The .mdp file for the run is as follows. The temperature plot has been
> attached with this mail.

Attachments are not accepted. You will need to upload to an online 
file-sharing provider and give a URL if you want to share such.

> define                 = -DFLEXIBLE
> constraints            = h-bonds
> integrator             = sd
> dt                     = 0.001          ; 1fs
> nsteps                 = 300000         ; 300 ps
> nstcomm                = 1
> nstxout                = 1000           ; frequency to write
> coordinates to output trajectory
> nstvout                = 0              ; frequency to write
> velocities to output trajectory; the last velocities are always
> written
> nstfout                = 0              ; frequency to write forces to
> output trajectory
> nstlog                 = 10             ; frequency to write energies
> to log file
> nstenergy              = 100 ; frequency to write energies to edr file
> nstcalcenergy          = 100
> vdwtype                = cut-off
> coulombtype            = cut-off

Excess heating from the artefacts of this method might be expected.

> pbc                    = no
> table-extension        = 20.0

This is much larger than you should need, but is not a problem. Do not 
attempt to work around 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up with this 
setting.

Mark

> nstlist                = 100
> ns_type                = grid
> rlist                  = 1.0
>
> rcoulomb               = 1.2
> rvdw                   = 1.2
>
> comm-mode              = angular
> comm-grps              = system
> optimize_fft           = yes
>
> ;heating
> annealing              = single
> annealing_npoints      = 2
> annealing_time         = 0 300
> annealing_temp         = 0 300
>
> ld_seed                = 8072012
>
> ; V-rescale temperature coupling is on
> Tcoupl = no
> tau_t = 0.02
> tc_grps = system
> ref_t = 0
>
> ; Pressure coupling is off
> Pcoupl = no
>
> ; Generate velocites is on
> gen_vel = yes
> gen_temp = 0
> gen_seed = 8042012
>