[gmx-users] Heating step by step.

[Mark Abraham]

Hi,

Not sure what the problem is, but you should start with a simple one step
annealing of one group. Get that right, then get complex.

Mark

On Sat, Sep 5, 2015 at 11:49 AM Dawid das <addiw7 at googlemail.com> wrote:

> I struggle to properly define my *mdp file. I have following keywords and
> their values:
>
> ;Simulated annealing is on
> annealing           = single
> annealing-npoints   = 30 30
> annealing-time      = 0.0 0.002 5.0 5.002 10.0 10.002 15.0 15.002 20.0
> 20.002 25.0 25.002 30.0 30.002 35.0 35.002 40.0 40.002 45.0 45.002 50.0
> 50.002 55.0 55.002 60.0 60.002 65.0 65.002  75.0 75.002 0.0 0.002 5.0 5.002
> 10.0 10.002 15.0 15.002 20.0 20.002 25.0 25.002 30.0 30.002 35.0 35.002
> 40.0 40.002 45.0 45.002 50.0 50.002 55.0 55.002 60.0 60.002 65.0 65.002
> 75.0 75.002
> annealing-temp      = 0 20 20 40 40 60 60 80 80 100 100 120 120 140 140 160
> 160 180 180 200 200 220 220 240 240 260 260 280 280 300 0 20 20 40 40 60 60
> 80 80 100 100 120 120 140 140 160 160 180 180 200 200 220 220 240 240 260
> 260 280 280 300
>
>
> ; Temperature coupling is on with annealing
> tcoupl          = V-rescale                 ; modified Berendsen thermostat
> tc-grps         = Protein non-Protein   ; two coupling groups - more
> accurate
> tau_t           = 0.1     0.1           ; time constant, in ps
> ref_t           = 300     300           ; reference temperature, one for
> each group, in K
>
> so I want to anneal two groups as you may see. However, grompp says:
>
> Fatal error:
> Not enough annealing values: 1 (for 2 groups)
>
> I believe I do everything according to the documentation.
>
> 2015-09-04 22:41 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
>
> >
> > 2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban <vvchaban at gmail.com>:
> >
> >> However, your simulation schedule makes little sense physically .
> >>
> >
> >
> > What do you mean by that? I just want to heat up my system gently before
> > equilibration phase.
> >
> --
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