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Messages - David Dubbeldam

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1
Visualization / Re: Visualisation using Para View
« on: February 03, 2020, 09:32:40 PM »
I guess you need to figure out how Paraview scales these. For the density file, it is by default 150x150x150 points, and this needs to be converted to the real unit cell.

2
Visualization / Re: Imported PDB file
« on: February 03, 2020, 09:25:16 PM »
There are many pdb-files out there that are not according to the PDB specification. You could try to use "openbabel" to create a good pdb-file and see if that works.

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
« 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.

6
General / Re: Flexible-MOFs forcefield Issue
« 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.

7
Output files / Re: Visualization of adsorption
« on: December 09, 2019, 08:54:35 AM »
You just import all the pdb- and cif-files you would like to visualize (so select multiple files during import).
Then you can set individual visualization properties, like origin, drawing-method, etc.

8
Either use a model that puts the charge-centers on the atomic centers (OPLS) or if the molecule is small you can also make the whole molecule rigid.

9
General / Re: Flexible-MOFs forcefield Issue
« on: November 08, 2019, 04:13:47 PM »
For a force field for a flexible MOF you need to define all the interactions similar to the flexible IRMOF-1 example.
The GenericMOFs defines only the interactions of molecules with the framework.

10
Simulation algorithms and theory / Re: MaxNumberOfCoulombicSites
« on: October 04, 2019, 01:18:16 PM »
You could do some basic debugging, like setting the PrintEvery to 1 and see if it is just slow or that you are really stuck at step 0.
The latter can happen if you try to put in more molecules than fit in the simulation volume.

11
Visualization / Re: Making the grid finer for adsorption surfaces
« on: October 03, 2019, 11:56:24 AM »
Currently it is using a grid of 128x128x128. Several opties are considered in future releases:
1) an option for 256x256x256
2) Use tessellation on newer videocards to create smoother surfaces.

12
Announcements / New review on force fields
« on: September 30, 2019, 06:41:57 PM »
An open access review that potentially could be of interest to some members on the forum, especially those that are interested in force fields, force field types and design, implementation (gradients, second derivatives, strain derivatives), Ewald summation, polarization, optimization, parameterization, Machine Learning, and General-Purpose GPU computing:
https://onlinelibrary.wiley.com/doi/10.1002/adts.201900135

13
Simulation algorithms and theory / Re: MaxNumberOfCoulombicSites
« on: September 29, 2019, 11:45:36 AM »
In open ensembles (Gibbs, grand-canonical ensemble) the number of molecules fluctuates. So if more memory is needed the code needs to realloc the memory to make it larger.

14
General / Re: Superimposing pdb files using iRASPA
« on: September 19, 2019, 07:00:13 PM »
Yes, just select both files when you import the structures.

15
General / Re: Status of iRASPA-QT
« on: September 18, 2019, 08:07:20 PM »
The windows/linux QT-versions has some basic functionality implemented (but still way less than the mac-version).
Windows QT version is available from the Windows store, and the linux version is available from the snap-store.

For both: good OpenGL >3.3 drivers are needed, and OpenCL drivers, which is a problem on both linux and windows.

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