[gmx-users] High density after NPT
schlecht at mail.ru
Thu Dec 20 01:28:00 CET 2012
I am trying to simulate a short protein (160aa) in water and after 500ps NPT
equilibration I got rather high value for density: average is 1014 and
pretty stable around this value, but quite noisy (peaks 1010-1020).
Also the pressure is very noisy with average about -7 (I am not sure it is
that bad since the fluctuations there are really big).
I used the AMBER03 FF with these settings for temperature and pressure
; Temperature Coupling
tcoupl = V-rescale
tc_grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure Coupling
pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
Previously made 100ps NVT equilibration (with modified Berendsen) gave
stable and quiet 300K.
What might be a problem here (if any)? Would it be better if I used
Nose-Hoover thermostat for temperature coupling (I suppose no as they both
are expected to give corrected ensembles)?
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