Simulated annealing (SA) settings

User discussions
1

GROMACS version: 2020.
GROMACS modification: No

Hello,
I want to perform SA runs to refine some protein-protein docking solutions and to determine the one with the minimum energy. I am playing with some settings for the SA, and I would appreciate some advice.
I have two coupling groups (Protein and Water_and_ions), 11 timepoints, and the total run is 50 ns.

annealing	= periodic periodic
annealing_npoints	= 11 11
annealing_time 	= 0    1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 0    1000 2000 3000 4000 5000 6000 7000 8000 9000 10000  ; time frame of heating/cooling cycles
annealing_temp	= 300  320	310  310  300  300	290	 290  280  280  275   300  320	310  310  300  300	290	 290  280  280  275    ; start and end temperatures

grompp (each cycle):

Time (ps)   Temperature (K)
      0.0      300.0
   1000.0      320.0
   2000.0      310.0
   3000.0      310.0
   4000.0      300.0
   5000.0      300.0
   6000.0      290.0
   7000.0      290.0
   8000.0      280.0
   9000.0      280.0
  10000.0      275.0

What do you think? Should I consider something else? I think 1 ns may be enough to reach the requested temperature and “allow for the inherent relaxation time in the coupling algorithm”, according to the manual.

Thanks in advance,
-Yasser