[gmx-users] Re: Problem with simulated annealing!!!

[Viswanadham Sridhara]

Hi Poornima,
If you can paste the entire mdp file, then it can be easy for the users to
suggest you things.
Cheers,

On 3/31/06, poornima Gajendrarao <poornings at yahoo.co.in> wrote:
>
> Dear Bruce,
>
> Thank you very much for your suggestion.
>
> I tried as you said. But the only difference Which I
> saw is that the temperautre goes upto 314 (I tried it
> with 10ps MDrun). After that I tried for 100ps MDrun.
> I used the same parameters which you have mentioned in
> the previous mail. I didnt change anything. And while
> running the grompp program for simulated annealing..
>
> I am getting these warnings:
>
> ARNING 1 [file full.mdp, line unknown]:
>   Unknown left-hand coulomb type in parameter file
>
> WARNING 2 [file full.mdp, line unknown]:
>   Unknown left-hand anneaing in parameter file
>
> WARNING 3 [file full.mdp, line unknown]:
>   Unknown left-hand anneling_npoints in parameter file
>
> can any one help to solve this problem!!
>
> Thanks in advance.
>
> with prayers,
> Poornima
>
>
>
>
>
> --- bfmilne at ff.up.pt wrote:
>
> > Hi Poornima,
> >
> > It could be that you are defining two
> > energy/temperature groups:
> > >tc-grps = Protein SOL
> > >tau_t = 0.1 0.1
> > >ref_t = 300 300
> > >; Energy monitoring
> > >energygrps = Protein SOL
> >
> > but then only defining annealing protocols for one
> > group:
> > >;simulated annealing
> > >anneling = single
> > >anneling_npoints = 5
> > >anneling_time = 2 4 6 8 10
> > >anneling_temp = 320 338 350 360 370
> >
> > I think it should be like this:
> >
> > annealing = single single
> > annealing_npoints = 5 5
> > annealing_time = 2 4 6 8 10 2 4 6 8 10
> > annealing_temp = 320 338 350 360 370 320 338 350 360
> > 370
> >
> > Have a look at the mdp options part of the online
> > manual and check the SA part.
> >
> > Cheers,
> >
> > Bruce
> >
> > --
> > Dr. Bruce F. Milne PhD
> > CEQOFFUP
> > Faculdade de Farmácia
> > Universidade do Porto
> > Rua Aníbal Cunha - 164
> > 4050-047
> > Porto
> > Portugal
> >
> >
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--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University,
Norfolk, VA-23529.
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