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 ." <sujithk...@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 <tsje...@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 ." <sujithk...@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. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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