[gmx-users] NPT - density off

[Mark Abraham]

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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