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
[EMAIL PROTECTED] 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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