[gmx-users] Setting up SA

[Seera Suryanarayana]

Dear gromacs users,

I have one peptide which has 25 residues. I have done simulation for 100ns.
When I presented my analysis in lab, I was suggested to do investigation of
my simulation by simulated annealing (SA). Then I have gone through the
simulated annealing notes which I found on gromacs website and I got some
idea to do simulated annealing. I added the annealing points and
temperatures in my .mdp file as follow.

;simulated annealing
annealing            = single
annealing-points  = 7
annealing-time    = 0 4000 8000 12000 16000 20000 24000
annealing-temp   = 300 310 315 330 320 310 300

What I want to do here is that first try to increase the temperature
gradually for some time then get it down to the reference temperature i.e
300K and allowed it to end of the simulation (100ns). Kindly tell me
whether my simulated annealing set up is correct.
Surya
Graduate student
India.