[gmx-users] Problems with SA: temp not changing

[David van der Spoel]

Monika Sharma wrote:
> Dear All,
> I am trying to minimize a protein using Simulated Annealing method 
> implemented in Gromacs3.3. I am giving the annealing points a 4 for temp 
> 400,350,300,250 for 10ps, but i am not getting the temperature change in 
> the log. Its just coming as 0 temperature only. I am using Langevin 
> dynamics for  temperature control. Here is my mdp file:
you have to turn on t coupling and probably you don't want the times to 
be identical at 10 ps either.
> 
> title           = TGR model minimization thru SA
> cpp             = /lib/cpp
> define          = -DFLEXIBLE
> constraints     = none
> integrator      = steep
> nsteps          = 50000
> dt                   =  0.02
> init_step       = 0
> ;langevin dynamics
> bd_fric         = 1
> ld_seed         = 1993
> ;minimization
> emtol           = 100
> emstep          = 1.0
> ;output control
> nstxout         = 100
> nstvout         = 100
> nstfout         = 100
> nstlog          = 100
> nstenergy       = 100
> nstxtcout       = 100
> xtc_precision   = 1000
> xtc_grps        =
> energygrps      =
> ; Neighbor searching
> nstlist         = 10
> ns_type         = grid
> pbc             = xyz
> rlist           = 1.5
> ; electrostatics
> coulombtype     = PME
> rcoulomb        = 1.5
> epsilon_r       = 1.0
> ; van der waals params
> vdwtype         = cutoff
> rvdw            = 2.0
> ; table params
> table-extension = 3
> ;PME params for ewald calc.
> fourierspacing  = 0.15
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ; temperature coupling
> tcoupl          = no
> ; pressure coupling
> pcoupl          = berendsen
> pcoupltype      = isotropic
> tau_p           = 1.2
> compressibility = 4.5e-5
> ref_p           = 1.01325
> ; simulated annealing params
> annealing       = single
> annealing_npoints = 4
> annealing_time  =  0   10    10    10
> annealing_temp  = 400  350  300  250
> ;velocity generation
> gen_vel           = no
> gen_temp        = 400
> gen_seed        = 1732529
> 
> If somebody can figure out what i am missing out, it will really be a 
> great help..
> thanks in advance,
> regards,
> Monika
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se