[gmx-users] Supercritical CO2

[Alex]

With opls-aa, incorrect densities and diffusivities were calculated
entirely away from the critical point for several liquids.

Alex
On May 1, 2015 11:40 AM, "V.V.Chaban" <vvchaban at gmail.com> wrote:

> This problem is natural. Even small change in (T,P) in the
> supercritical range results in a huge change of density and, hence,
> all other properties.
>
> You need either to alter (T,P) or to adjust the force field model
> (both change will be slight, but will bring large changes of density).
>
> If you expect any phase separation in these setups, take care of the
> Gibbs rule.
>
>
>
>
> On Thu, Apr 30, 2015 at 6:38 PM, Alex <nedomacho at gmail.com> wrote:
> > Only other suggestion I have is that 5 ns production runs are probably
> not
> > long enough. Granted, we needed diffusion data, so I believe I had 50 to
> > 100 ns long simulations, but even for the barostat to settle, it may be a
> > good idea to have simulations significantly longer than 5 ns.
> >
> > Alex
> >
> > On Thu, Apr 30, 2015 at 3:14 PM, Alex <nedomacho at gmail.com> wrote:
> >
> >> Unfortunately, I had a pretty terrible experience trying to simulate
> >> fuels, fuel mixtures, and CO2 dissolved in fuels with Gromacs (using
> >> OPLS-AA) at high pressures and/or temperatures. It is my understanding
> that
> >> at the moment this is isn't the area where these forcefields are
> seriously
> >> tested.
> >>
> >> I have no results for other forcefields, but for OPLS-AA it was
> >> unpublishable and came out as an internal note at the institution. If
> >> curious, see
> >> http://nvlpubs.nist.gov/nistpubs/TechnicalNotes/NIST.TN.1805.pdf
> >> In fact, if you get any results that correspond to experimental data,
> I'll
> >> really appreciate it if you let me know. :)
> >>
> >> Alex
> >>
> >> On Thu, Apr 30, 2015 at 2:04 PM, Jarrett Lee Wise <jwise6 at uwyo.edu>
> wrote:
> >>
> >>> Hello all-
> >>>
> >>> I am trying to run simulations containing supercritical CO2 and oil
> >>> asphaltenes.  I have tested various force fields (TraPPE flex, TraPPe
> >>> rigid, Charmm, EPM2, Cygan, and Zhang), but all of my results give
> either
> >>> extremely low densities (~200 kg/m^3) or extremely high densities
> (~1600
> >>> kg/m^3) when the density should be around 630 kg/m^3.
> >>>
> >>>
> >>> I equilibrated a system of 5000 CO2 molecules with Nose-Hoover and
> >>> Berendsen for 5 ns, then did a production run using Nose-Hoover and
> >>> Parrinello-Rahman for another 5 ns using 1 fs time step.
> >>>
> >>> I have found that tau_p plays an important factor.  A relaxed tau_p
> gives
> >>> low density while a vigorous tau_p gives a high density and crashes
> using
> >>> Parrinello-Rahman pressure coupling.
> >>>
> >>>
> >>> Has anyone else encountered similar problems or have any advice?
> >>>
> >>> Here is a copy of my MDP file.  Any advice is greatly appreciated.
> >>>
> >>> Thanks
> >>>
> >>>
> >>> Jarrett Wise
> >>> PhD Student
> >>> Petroleum Engineering
> >>> University of Wyoming
> >>>
> >>>
> >>> title           = CO2 Density Run
> >>> integrator      = md
> >>> nsteps          = 5000000
> >>> dt              = 0.001
> >>> nstxout         = 0
> >>> nstvout         = 0
> >>> nstfout         = 0
> >>> nstxtcout       = 20000
> >>> nstenergy       = 100
> >>> nstlog          = 1500
> >>>
> >>> constraint_algorithm = lincs
> >>> constraints     = H-Bonds
> >>> lincs_iter      = 1
> >>> lincs_order     = 4
> >>>
> >>> cutoff-scheme   = Verlet
> >>> ns_type         = grid
> >>> nstlist         = 100
> >>> rlist           = 1.4
> >>> rcoulomb        = 1.4
> >>> rvdw            = 1.4
> >>> nstcalcenergy  = 10
> >>> comm_mode = linear
> >>>
> >>> coulombtype     = PME
> >>> pme_order       = 4
> >>> fourierspacing  = 0.16
> >>>
> >>> tcoupl          = Nose-Hoover
> >>> tc-grps         = System
> >>> tau_t           = 5.0
> >>> ref_t           = 320
> >>>
> >>>
> >>> pcoupl          =  Parrinello-Rahman
> >>> pcoupltype      = isotropic
> >>> tau_p           = 3.0
> >>> ref_p           = 520.0
> >>> compressibility = 1.45e-4
> >>>
> >>> pbc             = xyz
> >>> continuation    = yes
> >>> gen_vel         = no
> >>> gen_temp       = 320
> >>>
> >>>
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> >>
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