I have a problem with interpretation of this mdp options.
title = MD equilibration;
dt = 0.002 ; 1 fs
nsteps = 5000000 ; 10 000 ps
ns_type = grid ; grid/simple (at the beg.)
; temperature coupling
tcoupl = berendsen ; nose-hoover/berendsen
tc-grps = SOL lipids
tau_t = 0.5 0.5 ;
ref_t = 310 310
; pressure
Pcoupl = berendsen ; parrinello-rahman/no/berendsen
Pcoupltype = anisotropic ; isotropic
tau_p = 0.5 0.5 0.5 0.0 0.0 0.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p = 1 1 1 0.0 0.0 0.0
;
So for example what does it mean "nose-hoover/berendsen".
At the beginning it starts with nose-hoover thermostat then berendsen??? From which step (I have 500000 steps)?
or parrinello-rahman/no/berendsen - so it starts with parrinello-rahman then no then berendsen ? From which step?