[gmx-users] High density after NPT

zugunder 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)?

Thank you.

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