On 20/08/2011 8:02 AM, Elisabeth wrote:
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.
These could reflect limitations in the model you are using (which almost
certainly wasn't parametrized upon data like this). Your integration
time step is twice as large as is commonly used in the absence of
constraints. Also, be sure you are measuring your density only after
equilibration, not an average that includes the equilibration period -
and describe that method so people here know you're making such sensible
measurements.
Mark
Thank you in advance for your invaluable help.
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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