[gmx-users] Simulated Annealing problem
Mark.Abraham at anu.edu.au
Sat Mar 22 11:40:12 CET 2008
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
> To check whether its because of temperature couple, t_coupling was
> removed. But then during .tpr formation, it complained of providing two
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
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