[gmx-users] Supercritical CO2

[Alex]

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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>
>