04 April 2019 0 9K Report

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?

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