[gmx-users] Simulated Annealing problem

[mon_sharma at research.iiit.ac.in]

On Sat, 22 Mar 2008, Mark Abraham wrote:

Hello,
Thanks for reply.
I am sorry for typo here, but just checked the .mdp file. Its correct 
in the input file.
In the log file, it says for annealing as:

grpopts:
    nrdf:             8093.62     55326.4
    ref_t:                300         300
    tau_t:                0.1         0.1
anneal:               Single      Single
ann_npoints:               7           7
ann. times [0]:          0.0       250.0       250.0       250.0 
250.0       500.0      1000.0
ann. temps [0]:        300.0       330.0       360.0       345.0 
330.0       315.0       300.0
ann. times [1]:          0.0       250.0       250.0       250.0 
250.0       500.0      1000.0
ann. temps [1]:        300.0       330.0       360.0       345.0 
330.0       315.0       300.0

By consistency, is it means equal intervals of time?

Regards,
Monika

> mon_sharma at research.iiit.ac.in wrote:
>> Dear All,
>> I am trying to do simulated annealing for solvated protein system.
>> the excerpts of the file is as:
>> 
>> energygrps               = protein non-protein
>> ;Temperature coupling
>> tcoupl                   = Berendsen
>> tc-grps                  = protein non-protein
>> tau_t                    = 0.1 0.1
>> ref_t                    = 300 300
>> ;Pressure coupling
>> Pcoupl                   = berendsen
>> Pcoupltype               = isotropic
>> tau_p                    = 1.0
>> compressibility          = 4.5e-5
>> ref_p                    = 1.0
>> ;Velocity generation
>> gen_vel                  = yes
>> gen_temp                 = 300
>> gen_seed                 = 173529
>> ; SIMULATED ANNEALING
>> ; Type of annealing for each temperature group (no/single/periodic)
>> annealing                = single single
>> ; Number of time points to use for specifying annealing in each group
>> annealing_npoints        = 7 7
>> ; List of times at the annealing points for each group
>> annealing_time           = 0 250 250 250 250 500 500 1000 0 250 250 250 250 
>> 500 1000
>> ; Temp. at each annealing point, for each group.
>> annealing_temp           = 300 330 360 345 330 315 300 300 330 360 345 330 
>> 315 300
>> 
>> The log however shows that the ref_t increase from 300K to 330K in 250ps 
>> and then it decreases to 300K in 750ps, and the temperature is aftwerwards 
>> maintained at 300K. From the input, it should increase to 360K and then 
>> decrease to 345,330,315 and 300K. But this is not happening.
>
> Read manual section 7.3.15 - the number of annealing_time entries is not 
> consistent.
>
>> To check whether its because of temperature couple, t_coupling was removed. 
>> But then during .tpr formation, it complained of providing two groups.
>
> Why haven't you copied and pasted the actual error message?
>
> This approach shouldn't work, as you would have expected if you'd read 
> section 3.7 of the manual.
>
>>  Will then SA wont take two groups (protein and non-protein)?
>> Why is it so then the temperature rises till 330 only, not after that, and 
>> it comes down?
>
> grompp should be describing the annealing profile it's doing. What did it 
> say?
>
> Mark
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