Dear Mr. Magnusl
Thank you for your nice suggestion.
The detailed information of the parameters I set is as follows. I set “emtol=50.0” when I do energy minimization and it converged. I used “V-rescale” as thermostat and “Berendsen” as barostat at the stage of equilibration. The “V-rescale” and “Parrinello-Rahman” was used at production MD, and tau_t=0.2, tau_p=2.0.
I will try to extend the equilibration simulations. I have a new question. Is prolonging the tau_p useful for maintaining system stability?
Looking forward to your reply.
The following is md.mdp:
integrator = md
dt = 0.002 ; ps
nsteps = 5000000 ; 10ns
comm-grps = DNA_Protein
comm-mode = angular
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 5000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-grps = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = EnerPres
;
Tcoupl = V-rescale
tau_t = 0.2 0.2
tc_grps = DNA_Protein Water_and_ions
ref_t = 298.15 298.15
;
Pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
;
constraints = hbonds