[gmx-users] temperature and pressure values

[Marino Convertino]

Hi all,
sorry for the long mail.
I am performing two different 45ps NPT equilibrations of an oligopeptide in water solvent (33157 system atoms), one with a temperature of 350K and the second one at 400K.


I am using this mdp with the gromos96 ff :

cpp = /lib/cpp
define = -DFLEX_SPC ; NPT 50 ps all free
constraints = all-bonds
constraint_algorithm= lincs
lincs_order = 8
integrator = md
dt = 0.0015
nsteps = 30000 ; total 45 ps.
nstxout = 6000
nstvout = 6000
nstfout = 0
nstlog = 6000
nstenergy = 500
nstxtcout = 6000
nstlist = 5
ns_type = grid
rlist = 0.8
coulombtype = cut-off
rcoulomb = 1.4
rvdw = 1.4
pbc = xyz
DispCorr = EnerPres
; Berendsen temperature coupling is on in two groups
Tcoupl = Berendsen
tc-grps = Protein SOL
tau_t = 0.1           0.1 ;time in ps
ref_t = 400           400
; Energy monitoring
energygrps = Protein SOL
; Isotropic pressure coupling is now on
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 1.0 ;time in ps
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 400 K.
gen_vel = yes
gen_temp = 400.0
gen_seed = 173529

And the same one mdp file  with 350K (ref_t and gen_temp).

Checking the md.log file I find in AVERAGES section:
- for 400K md: Temperature  4.03243e+02  and   Pressure (bar) 2.50459e+00 
- for 350K md: Temperature  3.53436e+02  and   Pressure (bar) 1.51139e+00

Can anyone tell me if this average values are ok for these kind of simulations?
If not, how can I obtain more precision in these analysis?
Thank a lot.
Marino Convertino 
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