Recent posts

#91

Simulation algorithms and theory / Re: How to do Monte Carlo simu...

Last post by David Dubbeldam - January 11, 2023, 08:05:51 PM

For running multiple simulations, you would use/create scripts that generate the needed input.
MOF simulations time depend on the size of the system, and how accurate you need the results.
Small systems, about a day. Larger system, a week or longer.

#92

Simulation algorithms and theory / How to do Monte Carlo simulati...

Last post by alireza_hadi68 - December 31, 2022, 07:00:36 AM

Hello everyone,

I want to work on a database containing a large number of MOFs, and I need their gas adsorption data (in a defined temperature and pressure). I am not familiar with RASPA and I want to learn it. There are lots of papers using RASPA for this purpose. I have some questions about this:
How could I use RASPA for a large number of MOFs?
Are there any algorithms to do simulations automatically?
How long does it take to do a simulation for each MOF?
What are the system requirements for such simulations?

Your answer could really help me.  :-[

Thanks!

#93

General / error message on restart after...

Last post by virginia314 - December 16, 2022, 02:27:38 AM

I am running a GCMC simulation for adsorption in a MOF that will run for several million steps. I wrote the binary restart file and when my job crashed, I tried to restart it. It read in the binary file and immediately crashed with this error:

read binary file
DONE!!!
Failed to Reposition output-file at 398119 ( beyond file-length 396809)

I tried running a small test case and the restart worked fine. What does this error mean?

#94

General / Re: About the relation between...

Last post by David Dubbeldam - December 02, 2022, 04:00:28 PM

For a detailed explanation see:
https://homepage.tudelft.nl/v9k6y/thesis-Rahbari.pdf
Page 262 and following, and see Table  A5.

#95

Simulation algorithms and theory / Re: can I simulate the adsorpt...

Last post by lzhzzz - November 30, 2022, 04:09:19 PM

That can not really be done without implementing that. The system must stay charge-neutral, so you cannot individually swap na and cl in and out. You will need to do that in pairs.

Hello dear David
If it is a neutral heavy metal molecule in solution, can it be calculated with raspa.
Thank you very much.

#96

Visualization / Re: Vector image export

Last post by David Dubbeldam - November 24, 2022, 10:55:40 AM

No, the data is inherently pixel-based. Exporting to pdf would just put a picture in a pdf.

#97

Visualization / Vector image export

Last post by cbornes - November 23, 2022, 05:40:09 PM

Hi

Is there a way to export a vectorial image from iraspa?

Best regards,
Carlos

#98

General / Re: About the relation between...

Last post by w_wonder - November 23, 2022, 12:13:59 AM

Thanks a lot. Sorry I am still confused  :'(

Would you provide any page number for McQuarrie8 used in Table S3 and/or calculation steps? Molecular thermal wavelength from https://en.wikipedia.org/wiki/Thermal_de_Broglie_wavelength is about 10^-11 m ~ 0.1 angstrom at 298K. q/\Lambda^3 ~ q/0.1^3 is unlikely to provide 10^100 for NH3, even varying mass and temperature.

#99

Announcements / RASPA workshop announced (onli...

Last post by David Dubbeldam - November 22, 2022, 10:37:09 AM

This workshop/school focused on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we were also considering the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online. Due to privacy reasons, there will be no video recordings. Registration is free but compulsory. Certificates of attendance will be made available after the workshop.
We are also planning offline workshops in 2023 (November, Abu Dhabi) and 2024 (September, The Netherlands).

https://iraspa.org/workshops/iraspa-raspa-online-workshop-2023/

#100

General / Re: About the relation between...

Last post by David Dubbeldam - November 22, 2022, 10:32:28 AM

These value come from: https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00092/suppl_file/ct7b00092_si_001.pdf
and to reduce under/overflow you input them as the log of these numbers in Table S3.