Dear all
I did some MC simulation to reproduce water adsorption isotherms on MOF-801 but results are not consistent at all. in the literature, water uptake at p/p0=0.2 is about 200 cm3/gr while mine is 0.5 cm3/gr. Molecule and force field definition is the same as literature. Partial charges were found beforehand using Qeq module and finalP1.cif file were used as the input cif. I also changed void fraction up to 0.9 but the impact is not so much! what did I miss? I appreciate any comment.
Regards
P. S. simulation file is as below:
SimulationType MonteCarlo
NumberOfCycles 50000
NumberOfInitializationCycles 10000
PrintEvery 10000
RestartFile no
chargemethod Ewald
Forcefield GenericMOFs
UseChargesFromCIFFile yes
cutoffvdw 12.0
SymmetrizeFrameworkCharges yes
Framework 0
FrameworkName mof-801-p1
UnitCells 2 2 2
HeliumVoidFraction 0.49
ExternalTemperature 298
ExternalPressure 3456
Component 0 MoleculeName water
MoleculeDefinition TraPPE
randomTranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
Are you comparing your simulation to other simulations or your simulations to experiments?
For the latter you need a bigger picture view and compare the simulated isotherm to the experimental one. Usually at some pressure the isotherm shoots up due to water-water clustering, but the details of where that happens depends on many factors (especially defects).
Also, the water-model is never perfect, nor is the force field in general.
Dear Dr. Dubbeldam
Thanks for the kind response. Actually I compare it with both simulated and experimental results which are consistent in previous literature. I compare my output with the examples of RASPA2 and I noticed that there were no more than 2 number of adsorbent in each cycle, while for example in the Adsorption_of_CO2_in_Flexible_IRMOF-1_Fixed_Volume, number of adsorbents in the last cycle is 39 and the excess loading is 140.3574056061 (avg. 158.7275906778) [cm^3 STP/g]. So I think there is something inhibiting a proper MC simulation. Moreover, I used psuedo_atom.def file to neutralized the charge of water molecules, however the MOF itself has a net charge. So I used randomTranslationProbability 0.5 and ReinsertionProbability 0.0 , but in the MC moves, charges were created on the water molecules (Net charge: 0.964176 (F: 0.000176, A: 0.964, C: 0)).
Here is the properties calculated at the last cycle of my simulation:
[Init] Current cycle: 900000 out of 1000000
========================================================================================================
Net charge: 0.964176 (F: 0.000176, A: 0.964, C: 0)
Current Box: 35.66960 0.00000 0.00000 [A]
0.00000 35.66960 0.00000 [A]
0.00000 0.00000 35.66960 [A]
Box-lengths: 35.66960 35.66960 35.66960 Box-angles: 90.00000 90.00000 90.00000 [degrees]
Volume: 45383.15846 [A^3]
Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (water), current number of integer/fractional/reaction molecules: 2/0/0, density: 1.31729 [kg/m^3]
absolute adsorption: 0.25000 [mol/uc], 0.0420 [mol/kg], 0.7563 [mg/g]
0.9417 [cm^3 STP/g], 1.6402 [cm^3 STP/cm^3]
excess adsorption: 0.25000 [mol/uc], 0.0420 [mol/kg], 0.7563 [mg/g]
0.9417 [cm^3 STP/g], 1.6402 [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 12 0 12 0
Number of Framework-atoms: 2624
Number of Adsorbates: 2 (2 integer, 0 fractional, 0 reaction)
Number of Cations: 0 (0 integer, 0 fractional, 0 reaction
Current total potential energy: -12224.3694682955 [K]
Current Host-Host energy: 0.0000000000 [K]
Current Host-Adsorbate energy: -14790.5805795910 [K]
Current Host-Cation energy: 0.0000000000 [K]
Current Adsorbate-Adsorbate energy: 2566.2111112939 [K]
Current Cation-Cation energy: 0.0000000000 [K]
Current Adsorbate-Cation energy: 0.0000000000 [K]
WARNING: THE SYSTEM HAS A NET CHARGE
Dear all
I test the same MOF adsorption isotherm of N2 at 77 K which behaved normal
Current cycle: 40000 out of 50000
========================================================================================================
Net charge: 0.000176 (F: 0.000176, A: 0, C: 0)
Current Box: 35.66960 0.00000 0.00000 [A] Average Box: 35.66960 0.00000 0.00000 [A]
0.00000 35.66960 0.00000 [A] 0.00000 35.66960 0.00000 [A]
0.00000 0.00000 35.66960 [A] 0.00000 0.00000 35.66960 [A]
Box-lengths: 35.66960 35.66960 35.66960 [A] Average: 35.66960 35.66960 35.66960 [A]
Box-angles: 90.00000 90.00000 90.00000 [degrees] Average: 90.00000 90.00000 90.00000 [degrees]
Volume: 45383.15846 [A^3] Average Volume: 45383.15846 [A^3]
Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (N2), current number of integer/fractional/reaction molecules: 302/0/0 (avg. 298.25187), density: 309.54848 (avg. 305.70667) [kg/m^3]
absolute adsorption: 37.75000 (avg. 37.28148) [mol/uc], 6.3438084017 (avg. 6.2650752004) [mol/kg], 177.7121497852 (avg. 175.5065588236) [mg/g]
142.1899676634 (avg. 140.4252435976) [cm^3 STP/g], 247.6738366201 (avg. 244.5999490094) [cm^3 STP/cm^3]
excess adsorption: 37.7474627383 (avg. 37.1564835879) [mol/uc], 6.3433820202 (avg. 6.2440692123) [mol/kg], 177.7002053553 (avg. 174.9181079965) [mg/g]
142.1804107585 (avg. 139.9544158901) [cm^3 STP/g], 247.6571899091 (avg. 243.7798369677) [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 1510 0 1510 0
Number of Framework-atoms: 2624
Number of Adsorbates: 302 (302 integer, 0 fractional, 0 reaction)
Number of Cations: 0 (0 integer, 0 fractional, 0 reaction)
Current total potential energy: -541892.7820463965 [K] (avg. -530686.6081954332)
Current Host-Host energy: 0.0000000000 [K] (avg. 0.0000000000)
Current Host-Adsorbate energy: -484779.4158412396 [K] (avg. -476688.6897432785)
Current Host-Cation energy: 0.0000000000 [K] (avg. 0.0000000000)
Current Adsorbate-Adsorbate energy: -57113.3662051579 [K] (avg. -53997.9184521721)
Current Cation-Cation energy: 0.0000000000 [K] (avg. 0.0000000000)
Current Adsorbate-Cation energy: 0.0000000000 [K] (avg. 0.0000000000)
WARNING: THE SYSTEM HAS A NET CHARGE
So I think something wrong about the water, maybe the increased charge of it in the MC simulation. Any comment?
Best regards
What do you mean with "there were no more than 2 number of adsorbent in each cycle", do you have multiple frameworks? do you mean "adsorbent" which is the framework, or "adsorbate" which means the molecules inside the framework.
"So I think something wrong about the water, maybe the increased charge of it in the MC simulation.", have you tried making it charge-neutral?