News:

SMF - Just Installed!

Main Menu
Menu

Show posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Show posts Menu

Messages - David Dubbeldam

#181
General / Re: Flexible-MOFs forcefield Issue
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.
#182
Output files / Re: Visualization of adsorption
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.
#183
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.
#184
General / Re: Flexible-MOFs forcefield Issue
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.
#185
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.
#186
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.
#187
Announcements / New review on force fields
September 30, 2019, 07:41:57 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
#188
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.
#189
General / Re: Superimposing pdb files using iRASPA
September 19, 2019, 08:00:13 PM
Yes, just select both files when you import the structures.
#190
General / Re: Status of iRASPA-QT
September 18, 2019, 09:07:20 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.
#191
Input files and parameters / Re: Raspa taking more time
September 12, 2019, 08:15:15 PM
For a comparison between some MC codes (Cassandra, DL Monte, Music, Raspa and Towhee) see:
https://www.tandfonline.com/doi/full/10.1080/08927022.2017.1375492

There is a wide difference in the statistical value of a single MC step, however their computational performance is quite comparable.

RASPA is not optimized for speed, and meant for relatively small system-sizes. The most expensive part is usually the Ewald-summation.
#192
Output files / Re: Histograms produced by raspa
August 31, 2019, 07:42:21 PM
Histograms do not really have units on the y-axis. The x-axis, for energy, would be Kelvin.
You can easily figure these things out by checking the source, and check what is exactly counted and how it is written out.
See source file: sample.c, and the function 'void SampleEnergyHistogram(int Switch)'.
#193
Saving of snapshots is more easily done by adding them to a movie. But you could run short simulations and copy the restart-file saved at the end to another directory if the goal is to create many restart-files.
#194
That is not possible. The atoms for the molecule file needs to be defined and the charge is taken from the pseudo_atoms.def file.
So, currently, the same type of atom of a molecule must have the same properties.
#195
You could add your way of computing the pressure in the source code, or modify the implemented calculation of the pressure.
SMF spam blocked by CleanTalk