[gmx-users] simulated annealing: what to do with ref_t? how slow is "slowly cooling"

[Kai Zhuang]

hi gromacs users:

i just started to play with simulated annealing for a protein system.
i noticed that there's a significant syntax change in gromacs 3.2 and
after... right? or am i just going crazy?

it seems to me that the older version, ref_t in temperature coupling
is used to control the annealing, which is now controlled by
annealing_temp.  but what do i do with ref_t now?


my planned scheme right now is as such:
1. heat from 300 to 1000K in 1ps
2. equilibriate for 200 ps (basically run MD for 200 ns)
3. lower from 1000 to 800K in 1 ns  (i'm not sure what is considered
"slow".  i have a pretty big system)
4. equilibriate for 200 ps 
5. lower from 800 to 600 in 1 ns
6. equilibriate for 200 ps 
7. lower from 600 to 400 in 1 ns
8. equilibriate for 200 ps 
9. lower from 400 to 300 in 1 ns
10. run MD for 5 ns

my mdp file looks like this:

title		=	SA 
cpp		=	/usr/bin/cpp
constraints	=	none
integrator	=	md
dt		=	0.001
nsteps		=	10000000  
nstcomm		=	1
nstxout		=	100
nstvout		=	500
nstfout		=	0
nstlist		=	5
ns_type		=	grid
pbc             =	xyz

; Energy Minimization
emtol                    = 10
emstep                   = 0.01
niter                    = 20
fcstep                   = 0
nstcgsteep               = 1000
nbfgscorr                = 10


;Electrostatic
coulombtype	=	PME
fourierspacing	=	0.12
pme_order	=	4
ewald_rtol	=	1e-5
optimize_fft	=	yes
	
rlist		=	0.9
rcoulomb	=	0.9
rvdw		=	1.4

;Temperature coupling
tcoupl		=	berendsen
tau_t		= 	0.1
tc-grps		=	protein
ref_t		=	300

; Pressure coupling
Pcoupl		=	berendsen
Pcoupltype	=	isotropic
tau-p		=	1.0
compressibility	=	4.5e-5
ref-p		=	1.0

;Simulated Annealing
annealing	=	single
annealing_npoints	=	10
annealing_time = 0 1 201 1201 1401 2401 2601 3601 3801 4801 
annealing_temp = 300 1000 1000 800 800 600 600 400 400 300

;Velocity Generation
gen_vel		=	yes
gen_temp	=	300
gen_seed	=	173529

-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789