Good day,
I have been trying to simulate self-diffusion of TIP4P2005 water in MIL125-Ti MOF at the limit of zero loading (i.e. infinite dilution).
I have 20 water molecules in my system but I have set up my simulation in such a way that adsorbate molecules do not interact with each other, thus resembling a case when we have only 1 molecule in the system. My problem with the results is two folds:
1.Considering I have only one type of molecule (i.e. water) in the system, both self-diffusion of water and self-diffusion of total fluid must be the same. However, the MSDs that I get for these two are not the same (as shown in Figure 1 of the attached excel file) which cannot be correct.
2. Because water molecules do not interact with each other, I expect my MSDs (and hence diffusivity coefficients) to be the same when they are averaged over all 20 molecules in the system and when they are calculated per molecule. But in my results they are different (as shown in Figure 2 of the attached excel file).
I was wondering, if I you could kindly give me a hint as where I might be making a mistake. or could this be a bug in the code?
Below I have provided a copy of my input file. The MSD results are also attached.
Thank you for your help in advance.
Best regards,
Amir
=========================
Simulation Input file:
SimulationType MolecularDynamics
NumberOfCycles 200000000
NumberOfInitializationCycles 10000
NumberOfEquilibrationCycles 50000
PrintEvery 1000
PrintPropertiesEvery 1000
RestartFile no
# Restart and crash-recovery
ContinueAfterCrash no # Write a binary file (binary restart.dat).
WriteBinaryRestartFileEvery 1000 # The output frequency of the crash-recovery file.
Ensemble NVT
Forcefield Water_MIL125_Ti
CutOffVDW 12.0
ChargeMethod Ewald #CoulombShifted or Ewald
CutOffChargeCharge 18.0
EwaldPrecision 1e-6
UseChargesFromCIFFile yes
OmitAdsorbateAdsorbateCoulombInteractions yes
OmitAdsorbateAdsorbateVDWInteractions yes
Framework 0
FrameworkName MIL125-Ti
UnitCells 2 2 2
ExternalTemperature 298.15
TimeStep 0.001
ComputeMSD yes
SampleMSDEvery 1000
PrintMSDEvery 1000
ComputeIndividualMSD yes
Movies yes
WriteMoviesEvery 1000
Component 0 MoleculeName TIP4P2005
StartingBead 0
MoleculeDefinition TIP4P2005
IdealGasRosenbluthWeight 1.00536
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 1.0
CreateNumberOfMolecules 20
=========================
I have been trying to simulate self-diffusion of TIP4P2005 water in MIL125-Ti MOF at the limit of zero loading (i.e. infinite dilution).
I have 20 water molecules in my system but I have set up my simulation in such a way that adsorbate molecules do not interact with each other, thus resembling a case when we have only 1 molecule in the system. My problem with the results is two folds:
1.Considering I have only one type of molecule (i.e. water) in the system, both self-diffusion of water and self-diffusion of total fluid must be the same. However, the MSDs that I get for these two are not the same (as shown in Figure 1 of the attached excel file) which cannot be correct.
2. Because water molecules do not interact with each other, I expect my MSDs (and hence diffusivity coefficients) to be the same when they are averaged over all 20 molecules in the system and when they are calculated per molecule. But in my results they are different (as shown in Figure 2 of the attached excel file).
I was wondering, if I you could kindly give me a hint as where I might be making a mistake. or could this be a bug in the code?
Below I have provided a copy of my input file. The MSD results are also attached.
Thank you for your help in advance.
Best regards,
Amir
=========================
Simulation Input file:
SimulationType MolecularDynamics
NumberOfCycles 200000000
NumberOfInitializationCycles 10000
NumberOfEquilibrationCycles 50000
PrintEvery 1000
PrintPropertiesEvery 1000
RestartFile no
# Restart and crash-recovery
ContinueAfterCrash no # Write a binary file (binary restart.dat).
WriteBinaryRestartFileEvery 1000 # The output frequency of the crash-recovery file.
Ensemble NVT
Forcefield Water_MIL125_Ti
CutOffVDW 12.0
ChargeMethod Ewald #CoulombShifted or Ewald
CutOffChargeCharge 18.0
EwaldPrecision 1e-6
UseChargesFromCIFFile yes
OmitAdsorbateAdsorbateCoulombInteractions yes
OmitAdsorbateAdsorbateVDWInteractions yes
Framework 0
FrameworkName MIL125-Ti
UnitCells 2 2 2
ExternalTemperature 298.15
TimeStep 0.001
ComputeMSD yes
SampleMSDEvery 1000
PrintMSDEvery 1000
ComputeIndividualMSD yes
Movies yes
WriteMoviesEvery 1000
Component 0 MoleculeName TIP4P2005
StartingBead 0
MoleculeDefinition TIP4P2005
IdealGasRosenbluthWeight 1.00536
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 1.0
CreateNumberOfMolecules 20
=========================