[gmx-users] Simulated Annealing General Procedure

[Neena Susan Eappen]

Hello gromacs users,

My goal is to do a better conformational sampling of my peptides using simulated annealing. Is my following procedure correct?

1- Energy minimization
2- NVT equilibration with position restraints say at 600 K for 100 ps
3- Simulated annealing with position restraints to cool down from 600 K to 300 K for 152 ps, with no velocity generation
4- Production simulation at 300 K for 10 ns without position restraints, with no velocity generation
5- Another step of energy minimization
6- Then repeat steps 2-6 multiple times with initially minimized structure from step 1

Many thanks,
Neena