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Attempted to delete molecule X of species 2 but the molecule energy is too high
- sarvelos
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6 years 7 months ago #397
by sarvelos
Hi!
I have been trying to simulate the adsorption on zeolites which have non-orthorhombic structures and I have not been able to. I have had problems with the following error "Attempted to delete molecule XXX of species 2 but the molecule energy is too high; This error occurred in subroutine Deletion on step XXXXX”... I tried to perform the simulations in Cassandra version 1.1 and overlaps were detected during the simulation. What could be happening? Attached is the 18 uc (3x3x2) files of DDR zeolite, each unit has 360 atoms, with a = 13.7950 Å, b = 13.7950 Å, c = 40.7500Å, α = 90.000°, β = 90.000°, γ = 120.000°. The attached simulation represents the adsorption at 298.15 K and chemical potentials of 40 and 35 kJ / mol of CO2 (pressures of 1.15 and 7.18 bar, respectively). I have tried to simulate other structures for which at least one of the angles is different from 90 ° and the same problem happens.
I know the problem is with the format of the box and not with the structure ... I already tried to perform a density calculation in canonic ensemble (nvt) for CO2 in a non-orthorhombic box (see files in the densitytest folder) and, despite of the equilibrium pressure to be kept as expected according with NIST, very high out of order values of pressure are obtained during the simulation (see file prp).
Thank you for your attention! Sarah
I have been trying to simulate the adsorption on zeolites which have non-orthorhombic structures and I have not been able to. I have had problems with the following error "Attempted to delete molecule XXX of species 2 but the molecule energy is too high; This error occurred in subroutine Deletion on step XXXXX”... I tried to perform the simulations in Cassandra version 1.1 and overlaps were detected during the simulation. What could be happening? Attached is the 18 uc (3x3x2) files of DDR zeolite, each unit has 360 atoms, with a = 13.7950 Å, b = 13.7950 Å, c = 40.7500Å, α = 90.000°, β = 90.000°, γ = 120.000°. The attached simulation represents the adsorption at 298.15 K and chemical potentials of 40 and 35 kJ / mol of CO2 (pressures of 1.15 and 7.18 bar, respectively). I have tried to simulate other structures for which at least one of the angles is different from 90 ° and the same problem happens.
I know the problem is with the format of the box and not with the structure ... I already tried to perform a density calculation in canonic ensemble (nvt) for CO2 in a non-orthorhombic box (see files in the densitytest folder) and, despite of the equilibrium pressure to be kept as expected according with NIST, very high out of order values of pressure are obtained during the simulation (see file prp).
Thank you for your attention! Sarah
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6 years 7 months ago #417
by jshah
I see that the CO2 mcf file contains a single LJ particle. Are you using a united-atom force field for CO2? How well does the force field perform in predicting pressures? Have you tried CO2 density calculations in a cubic simulation box?
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