[gmx-users] Problems with CO2-water simulation
Tsjerk Wassenaar
tsjerkw at gmail.com
Mon Dec 8 08:41:24 CET 2014
Hi Sujith,
Yes, you're right :) Nonetheless, there's nothing intrinsically odd about a
positive potential energy. Still, I also think that there will be a
considerable portion of carbonate. I think it's good to be suspicious of
such reactions in classical simulations.
Cheers,
Tsjerk
On Dec 8, 2014 8:23 AM, "sujithkakkat ." <sujithks58 at gmail.com> wrote:
> Hello Tsjerk,
>
> Thanks for the response. I find your argument intuitive. But my
> simulations are at 30bars and 250K. Isn't the conditions supposed to play a
> role in making the dissolved state metastable. My system at 250K and 30
> bar is like a closed coke can in the refrigerator. I believe there are no
> bubbles in the coke can until we open it to release the pressure.
>
> Also, I have performed simulations with methane-water systems at similar
> conditions. There I found the potential energy is negative. Since , I guess
> CO2 to be more soluble in water, doesn't that make the positive potential
> energy in CO2-water case unusual.
>
> Regards,
> Sujith.
>
> On Mon, Dec 8, 2014 at 12:35 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Sujith,
> >
> > There is nothing special about positive potential energy. In this case it
> > explains why soft drinks gives bubbles: the CO2 wants to get out. In
> > addition, if it could, it would drive the system to HCO3-/H3O+, which is
> an
> > energetically more favorable way to store CO2 in water.
> >
> > Cheers,
> >
> > Tsjerk
> > On Dec 8, 2014 6:50 AM, "sujithkakkat ." <sujithks58 at gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I am trying to simulate a water-carbondioxide system at 250K and
> > > 30bar. The system consists of 85 CO2 and 1204 water molecules in a
> 3x3x4
> > nm
> > > box.
> > >
> > > I used EPM2 and TIP4P potentials for CO2 and water following
> > > *Energy
> > > Environ. Sci., 2012, 5, 7033-7041* where the authors used the same.\
> > >
> > > I am facing problems with the energy potential energy values
> which
> > > are very high and positive ( of the order 10^7).
> > >
> > > I tried the same simulation with the OPLSAA topology of CO2
> which
> > I
> > > obtained from Dr. Justin Lemkul's tutorial on virtual site with TIP4P
> > > water. The problem still remains, potential energy values being highly
> > > positive.
> > >
> > > I am totally stuck at this point and is unable to find how to
> > tackle
> > > the problem.
> > >
> > > Firstly, I am wondering whether the positive potential energy is
> > > something to be worried about. If so, it would be great if you could
> > > provide me some direction in which I should think, or suggest me
> > something
> > > to read about on this issue.
> > >
> > > Given below is the parameter file I used (I have redueced the
> step
> > > size due to a avoid persistent blowing up problem);
> > >
> > > title = co2--in-water
> > >
> > > ; Run parameters
> > > integrator = md
> > > nsteps = 2500000
> > > dt = 0.0002
> > >
> > > ; Output control
> > > nstxout = 5000
> > > nstvout = 5000
> > > nstenergy = 5000
> > > nstlog = 5000
> > > nstxtcout = 5000
> > >
> > > ; Bond parameters
> > > continuation = no
> > > constraint_algorithm = lincs
> > > constraints = all-bonds
> > > lincs_iter = 2
> > > lincs_order = 4
> > >
> > > ; Neighborsearching
> > > cutoff-scheme = Verlet
> > > ns_type = grid
> > > nstlist = 10
> > > rcoulomb = 1.2
> > > rvdw = 1.2
> > >
> > > ; Electrostatics
> > > coulombtype = PME
> > > pme_order = 4
> > > fourierspacing = 0.16
> > >
> > > ; Temperature coupling is on
> > > tcoupl = Nose-Hoover
> > > tc-grps = CO2 SOL
> > > tau_t = 0.4 0.4
> > > ref_t = 250 250
> > >
> > > ; Pressure coupling is on
> > > pcoupl = Parrinello-Rahman
> > > pcoupltype = isotropic
> > > tau_p = 2.0
> > > ref_p = 30.0
> > > compressibility = 4.5e-5
> > > refcoord_scaling = com
> > >
> > > ; Periodic boundary conditions
> > > pbc = xyz
> > >
> > > ; Dispersion correction
> > > DispCorr = EnerPres
> > >
> > > ; Velocity generation
> > > gen_vel = no
> > > gen_temp = 250
> > > gen_seed = -1
> > >
> > >
> > >
> > > The EPM2 topology file which I made is given below;
> > >
> > > [atomtypes]
> > > ; name mass charge ptype sigma epsilon
> > > D 22.0049 0.0000 A 0.0000 0.0000
> > > CA 0.0000 0.6512 A 0.2757 0.2339
> > > CO 0.0000 -0.3256 A 0.3033 0.6695
> > >
> > > [moleculetype]
> > > ; name nrexcl
> > > CO2 2
> > >
> > > [atoms]
> > > ; nr type resnr residue atom cgnr charge mass
> > > 1 D 1 CO2 D1 1 0.0000 22.0049
> > > 2 D 1 CO2 D2 1 0.0000 22.0049
> > > 3 CA 1 CO2 CA 1 0.6512 0.0000
> > > 4 CO 1 CO2 OC1 1 -0.3256 0.0000
> > > 5 CO 1 CO2 OC2 1 -0.3256 0.0000
> > >
> > > [constraints]
> > > ; i j funct doc
> > > 1 2 1 0.195948
> > >
> > > [virtual_sites2]
> > > ; i j k funct a
> > > 3 1 2 1 0.5
> > > 4 1 2 1 1.08638006
> > > 5 2 1 1 1.08638006
> > >
> > >
> > >
> > > Regards,
> > >
> > > Sujith.
> > > --
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