[gmx-users] Another problem with Stimulated Annealing

[Monika Sharma]

Thanks for your reply. So what you meant by it, that the steep option 
will always be at 0K. and what this gen_temp will corresponds to??  and 
SA wont have meaning for steep.  Can you please help me in understanding 
some things?
1. md integrator wont be a good option for minimization? since it can 
take different temperature.
2. steep integrator will work on temp 0K only, whatsoever the 
temperature couple or velocity generation value we provide??
These seems to be baffling.. what to use first and how to proceed??  I 
have gone through manual and tutorials, but still seems confused.
Please do suggest...
regards,
Monika
David van der Spoel wrote:

> 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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