[gmx-users] Simulated Annealing problem

[Mark Abraham]

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