[gmx-users] Another problem with Stimulated Annealing

[David van der Spoel]

Monika Sharma wrote:
> Dear All,
> While doing SA, I am observing that when i am using steep as option for 
> minimization, then the md log file generated takes ref_t as 0K temp 
> only, but when i am using md as integratore, the temp for ref_t is taken 
> as 375K( temp i gave).. See below... Its quite strange....

there is no temperature in a minimization.



> +++++++++++++++++++++++++++++++++++++
> log file with steep as integrator:
> ------------------------------------- grpopts:
>   nrdf:             27419.8      451854
>   ref_t:                  0           0
>   tau_t:                  0           0
> anneal:               Single      Single
> ann_npoints:               4           4
> ann. times [0]:          0.0         2.0         4.0         6.0
> ann. temps [0]:        375.0       350.0       325.0       300.0
> ann. times [1]:          0.0         2.0         4.0         6.0
> ann. temps [1]:        375.0       350.0       325.0       300.0
>   acc:            0           0           0
>   nfreeze:           N           N           N
> ---------------------------------
> -++++++++++++++++++++++++++++++++++++++++++++++
> log file with md as integrator:
> ---------------------------------------------------------
> grpopts:
>   nrdf:             27419.8      301239
>   ref_t:                375         375
>   tau_t:                0.1         0.1
> anneal:               Single      Single
> ann_npoints:               4           4
> ann. times [0]:          0.0         2.0         4.0         6.0
> ann. temps [0]:        375.0       350.0       325.0       300.0
> ann. times [1]:          0.0         2.0         4.0         6.0
> ann. temps [1]:        375.0       350.0       325.0       300.0
>   acc:            0           0           0
>   nfreeze:           N           N           N
> _--------------------------------------------------------------------------- 
> 
> 
> The mdp file is same for both but only diff is the integrator..
> Here is mdp file:
> title           =
> cpp             = /lib/cpp
> define          = -DFLEXIBLE
> constraints     = none
> integrator      = steep (here the only diff as md)
> nsteps          = 5000
> dt              = 0.02
> init_step       = 0
> ;langevin dynamics
> bd_fric         = 0
> ld_seed         = 1993
> ;minimization
> emtol           = 100
> emstep          = 1.0
> ;output control
> nstxout         = 10
> nstvout         = 10
> nstfout         = 10
> nstlog          = 10
> nstenergy       = 10
> nstxtcout       = 10
> xtc_precision   = 100
> 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          = berendsen
> tc-grps         = protein non-protein
> tau_t           =  0.1     0.1
> ref_t           =  375     375
> ; pressure coupling
> pcoupl          = berendsen
> pcoupltype      = isotropic
> tau_p           = 1.2
> compressibility = 4.5e-5
> ref_p           = 1.01325
> ; simulated annealing params
> annealing       = single single
> annealing_npoints = 4     4
> annealing_time  =  0   2    4    6     0    2   4   6
> annealing_temp  =  375 350  325  300  375 350  325  300
> ;velocity generation
> gen_vel         = no
> gen_temp        = 375
> gen_seed        = 1732529
> ------------------------------------------------------------------------------------------------------------------- 
> 
> So my ques is that does that really means that SA works with md only, 
> not steep. Is it a bug or some reason behind it?? I have not come across 
> any... but with md run I am not getting any value. the run is crashing, 
> only the steep is showing some output, but that at 0K??
> Can someone suggest anything for a succesful SA-MD?
> 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