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1
Bug reports / Re: MSD for diffusion at infinite dilution
« Last post by Amir on January 17, 2020, 05:31:03 PM »
Apparently, the website doesn't allow me to upload my attachments! I can provide them via direct contact to anyone who is happy to have a look. Thanks you :)
2
Bug reports / MSD for diffusion at infinite dilution
« Last post by Amir on January 17, 2020, 05:23:02 PM »
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

=========================
3
Chemical potentials and fugacities are related by a trivial conversion and represent the same concept.
Fugacity is easier to use because it is always a positive number, while the chemical potential goes to minus infinity at infinite dilution.
Fugacity also has a more direct relation to pressure.
4
Simulation algorithms and theory / Re: about CFCMC potential
« Last post by David Dubbeldam on January 16, 2020, 06:17:31 PM »
Energies are capped at high values to avoid numerical artifacts. In CFCMC, you can also use a small distance overlap criteria (as in the original CFCMC work of the Maginn-group).
5
You need a good force field to reproduce the correct occupancy. Also, the simulations are non-trivial and some people use parallel-tempering to compute the proper occupancy distributions.
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General / Re: Flexible-MOFs forcefield Issue
« Last post by David Dubbeldam on January 16, 2020, 06:13:10 PM »
The interactions are up to you. Bond-potentials and bend-potentials between the atoms are common, but force fields differ in the treatment of torsion-and improper torsion potentials, and VDW and electrostatics.
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Input files and parameters / Question on how to describe ions' chemical potential
« Last post by Haolong on January 09, 2020, 05:34:13 AM »
Hi, Professor David:

How can I describe ions' chemical potential instead of fugacity, which is mainly used to describe the property of gas, in the input file? :)

Kind regards,
Haolong
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General / Re: Flexible-MOFs forcefield Issue
« Last post by Hattuck on January 02, 2020, 03:14:15 PM »
Is there anywhere a list of all the interactions that you need to define for this to work?
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Input files and parameters / Error while using supercelled structure
« Last post by jeonghyeon on December 25, 2019, 09:34:18 AM »
Dear Prof. Dubbeldam,

Currently, I am running raspa with ZIF-7 structure, which has triclinic unit cell.

When I conducted energy minimization and NPT MD simulations using this structure with 'UnitCell 1 1 1' command, the program gave me good results as I expected.

However, as I changed the UnitCell command from 1 1 1  to 1 1 2 or other supercelled one, the program was just stopped, and the reason was strange coulombic interaction energy.

When I compared the energy contributions summarized in the output file, all other energies were multiples of those of unitcell except for 'Host/Host Coulomb energy'.

Can you help me to solve this problem?

Best regards,
Jeong Hyeon.
10
Simulation algorithms and theory / about CFCMC potential
« Last post by zhaoli2023 on December 20, 2019, 04:48:57 AM »
Hi Professor Dubbeldam,
I wonder is there a specific reason why energies are capped when using CFC (in potentials.c, PotentialValue function)? Is that because CF energies are harder to evaluate than traditional LJ 12-6?

Thanks for your help!!!
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