# [gmx-users] NPT - density off

Elisabeth katesedate at gmail.com
Sun Aug 21 06:08:27 CEST 2011

```On 20 August 2011 21:20, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

>  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.
>

Hello Mark,

Thank you for your comment. Densities are equilibrated. I am not sure what
you mean by limitations in the model. I actually fixed the density and tried
NVT using the experimental density at 298 and found a full agreement between
vaporization heat of the liquid and that reported in the original OPLS
paper. Once I try to obtain the density using NPT this inaccuracy in
densities appear. I have been using 1 fs dt with berendsen barostat for 5 ns
and collected data over the last 1 ns ( there are about 2500 atoms in the
system). So now I am going to follow your instruction and try dt of 0.5 fs
for another 5ns along with cpt files from previous barostat trial
(berendsen). I will get back to you to report the results soon.

BTW: I am using version 4.5.4

Thank you,

>
> Mark
>
>
> 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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