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Messages - David Dubbeldam

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1
General / Re: Problems installing on Ubuntu
« on: April 08, 2021, 04:19:10 PM »
Apparently, the new Ubuntu removed sysctl. I have replaced sysctl by uctsname.
Please update to v2.0.42, and check whether it now works for you on Ubuntu 20.10.

2
Visualization / Re: Get channel and cages from zeolites in iRaspa
« on: April 08, 2021, 10:00:31 AM »
Drag the MFI-example to your local projects so that it is editable. Then select the channel in the 'Scene Navigator' (See help).
After that go to the detail-view called 'Appearance' on the right, and set the properties of the 'primitive' (like the color and shape/size of the cylinder primitive).

3
Visualization / Re: Get channel and cages from zeolites in iRaspa
« on: March 25, 2021, 03:13:45 PM »
It is a standard example of iRASPA. It is in the gallery examples.
Gallery -> Primitives -> MFI

4
General / Re: ForceField Parameter for Carbon
« on: March 06, 2021, 06:29:26 PM »
The potential is defined differently in DREIDING. If you use it in the formula of the LJ with the most common form, then you need to convert sigma.

5
Output files / Re: Output file in CIF format = MOFs + guests
« on: March 06, 2021, 06:27:09 PM »
What is the start point, do you already have the two cif files? You could then just add the content of the atoms to the other (if they have the same unit cell information).
if you have for example pdb's then use a converting program like openbabel.

6
Input files and parameters / Re: Density histograms
« on: February 12, 2021, 11:07:08 AM »
I do not think there is a such a function. Always check the output file whether it corresponds to your input.
There is a setting "ComputeEnergyHistogram" or "ComputeDensityProfile3DVTKGrid".

7
General / Re: The Tail-Correction in RASPA
« on: February 12, 2021, 11:00:58 AM »
It would be inconsistent if the host-host contribution would be ignore. The large value is because you have a lot of VDW pairs in the framework.
Note: if a particle moves from A to B, in the energy difference that value cancels out. So it has little influence on adsorption, only via the positions of the framework atoms.

8
Importing and exporting / Re: Load bonds from file?
« on: February 04, 2021, 02:00:29 PM »
No, the bonds are not read, and dynamically recomputed. VMD can read the bonds from file I think (without recomputing them).

9
General / Re: Number of molecules in GEMC box
« on: February 04, 2021, 01:58:58 PM »
The number of molecules in Gibbs is an input parameter. Usually you want a sufficient number of molecules to reduce finite size effects (like 256 or 512) in liquid/vapor equilibrium Gibbs.
In case of adsorption, you need more molecules that the saturation loading in the framework plus then enough molecules in the vapor phase.

10
Simulation algorithms and theory / Re: Simulated Annealing
« on: January 19, 2021, 07:22:56 PM »
No, but you could achieve this with scripts. Just simulate at a certain temperature, and use the restart-file to restart at a lower temperature.

11
Note that force fields like 'GenericMOFs' are only examples (just like any molecule or structure file), just for the example cases in the code to work. For any real work you need to create and develop your own force fields, or take them from from the literature, and carefully construct, check and validate them.

12
Also, orthorhombic is much faster than triclinic. For triclinic structure, the distance computation is a matrix multiplication to get fractional coordinates, then apply periodic boundary conditions, and then convert back to Cartesian space.

13
It might be that if you choose the atomic positions wrong, that the molecules can overlap. This happened in particular with for example water where the larger oxygen shield the hydrogens. Often the hydrogens do not have a VDW parameter because the repulsion of the oxygen is sufficient. Choosing a wrong repulsion (too small sigma) leads to overlap with the hydrogens and hence numerical issues. So with classical force fields you should always be aware and avoid unphysical situations.

14
General / Re: Warning: Reinsertion used on the charged ions
« on: January 07, 2021, 08:02:11 PM »
The reason for the warning is that using CBMC with regrow is not advisable when the molecule has a net charge. The energies could become why to small/large leading to under/overflow.
It is better than for cations to use 'random translation'.

If the net-charge changes it can be because the adsorbate has a (small) net charge. With inserting adsorbates it will then grow in magnitude.

15
Input files and parameters / Re: Change input file when restart
« on: January 07, 2021, 07:58:34 PM »
Using the 'binary' file, the simulation should immediately end, since it was already finished. There is no wya to extend a binary restart.
The other form of restart just use the initial positions written as output from the previous run.
The positions are written to 'Restart', while reading is from 'RestartInitial' to avoid overwriting these.
To restart, copy 'Restart' to 'RestartInitial'.
If results are different, then you did not equilibrate long enough.

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