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

[poornima Gajendrarao]

Hai all,

This is my simulated annealing mdp file.. 

title               =  simulated annealing test run
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  50000    ; total 100 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  500
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulomb type        =  PME
rcoulomb            =  0.9
rvdw                =  1.4
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  system
tau_t               =  0.5
ref_t               =  300
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  5.0
compressibility     =  4.5e-5
ref_p               =  1.0
;simulated annealing
anneaing            = single, single
anneling_npoints    = 5,5
annealing_time      = 20 40 60 80 100 20 40 60 80 100
annealing_temp      = 320 338 350 360 370 320 338 350
360 370

; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529



--- Viswanadham Sridhara <muta.mestri at gmail.com>
wrote:

> 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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