# [gmx-users] NPT - density off

Elisabeth katesedate at gmail.com
Sat Aug 20 00:02:59 CEST 2011

```Dear experts,

I am intending to calculate the equilibrium density of a pure hydrocarbon at
different pressures , at 425 K. The normal boiling point of the liquid is
around 350 K. For pressures below 100 bar densities I am getting from NPT is
in accurate. I start form a structure which is compressed to above 0.6 g/cm3
density but since temperature is high density goes than to the values
below.

P = 50 bar > NPT rho=   0.344   experimental density ~ 0.54
P    100      >     NPT rho=  0.43      experimental density ~ 0.55

densities become more accurate for P >100 bar.

P     500    >   rho=  0.56    experimental density ~ 0.61

I thought maybe you have some idea on how this inaccuracy can be improved.

Best,

;        Bonds
constraints             = none
constraint-algorithm = lincs

;        Run control
integrator          =  md
dt                  =  0.001
nsteps              =  5000000
nstcomm             =  100

;        Output control
nstenergy           =  100
nstxout             =  100
nstvout             =  0
nstfout             =  0
nstlog              =  1000
nstxtcout          =  1000

;        Neighbor searching
nstlist             =  10
ns_type             =  grid

;        Electrostatics/VdW
coulombtype         =  Shift
vdw-type            =  Shift
rcoulomb-switch     =  0
rvdw-switch         =  0.9

;        Cut-offs
rlist               =  1.25
rcoulomb            =  1.0
rvdw                =  1.0

;        Temperature coupling
Tcoupl              =  v-rescale
tc-grps             =  System
tau_t               =  0.1
ref_t               =  425

;        Pressure coupling
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  1
compressibility     =  3.5e-5
ref_p               =  100

;        Velocity generation
gen_vel             =  no;yes
gen_temp            =  425
gen_seed            =  173529
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