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
<[EMAIL PROTECTED]> 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
--- [EMAIL PROTECTED] 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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