[gmx-users] Problems with CO2-water simulation
sujithkakkat .
sujithks58 at gmail.com
Mon Dec 8 08:23:04 CET 2014
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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