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#21
Input files and parameters / Re: Crash restart
Last post by trannghia207 - December 05, 2024, 06:20:53 AMI got the same problem when switching between different systems. It looks like the binary cannot be read if the architectures of the CPUs are different. But this may be not true.
#22
General / Monte carlo on biomolecules
Last post by mms - November 28, 2024, 09:27:52 AMHi Prof. Dubbeldam,
I am new to RASPA, so so please forgive any oversights and ignorance from my part.
Can raspa do monte carlo simulations on biomolecules like protein or rna? I want to study the binding of ions using Monte carlo. If not, can you please suggest me another software?
I am new to RASPA, so so please forgive any oversights and ignorance from my part.
Can raspa do monte carlo simulations on biomolecules like protein or rna? I want to study the binding of ions using Monte carlo. If not, can you please suggest me another software?
#23
Input files and parameters / Help with Simulating Henry's C...
Last post by jemilu - November 27, 2024, 10:02:20 AMDear RASPA Community,
I am a beginner with RASPA and am working on simulating the solubilities of methane and carbon dioxide in water using Monte Carlo methods. Following the RASPA manual, I have set up my simulation as follows:
Water Equilibration:
I used molecular dynamics to equilibrate water molecules at 298 K and 1 atm.
Monte Carlo Simulation:
Methane and carbon dioxide insertion/deletion was performed using the input below:
SimulationType MonteCarlo
NumberOfCycles 50000
NumberOfInitializationCycles 5000
PrintEvery 1000
RestartFile yes
ChargeMethod Ewald
Box 0
BoxLengths 25.10759 25.10759 25.10759
BoxAngles 90 90 90
ExternalTemperature 298
ExternalPressure 101325
ComputeMoleculeProperties yes
ComputeMolecularPressure yes
ComputeMSD yes
PrintMSDEvery 5000
Movies yes
WriteMoviesEvery 100
ComputeRDF yes
writerdfevery 1000
Component 0 MoleculeName water
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
VolumeChangeProbability 0.1
CreateNumberOfMolecules 0
Component 1 MoleculeName methane
TranslationProbability 0.5
RotationProbability 0.5
CFSwapLambdaProbability 1.0
CreateNumberOfMolecules 0
WidomProbability 1.0
I included WidomProbability to compute Henry's coefficient, as described in the manual. However, the Henry's coefficient does not appear in the output. I suspect this might be due to water being a high-density liquid rather than a porous material like a MOF.
My main question is:
How can I calculate the Henry's coefficient for methane and carbon dioxide in water at varying pressures using RASPA?
This coefficient is essential for applying Henry's law to determine partial pressures for my research.
Thank you in advance for your guidance.
Best regards,
Jemilu Omeje Audu
I am a beginner with RASPA and am working on simulating the solubilities of methane and carbon dioxide in water using Monte Carlo methods. Following the RASPA manual, I have set up my simulation as follows:
Water Equilibration:
I used molecular dynamics to equilibrate water molecules at 298 K and 1 atm.
Monte Carlo Simulation:
Methane and carbon dioxide insertion/deletion was performed using the input below:
SimulationType MonteCarlo
NumberOfCycles 50000
NumberOfInitializationCycles 5000
PrintEvery 1000
RestartFile yes
ChargeMethod Ewald
Box 0
BoxLengths 25.10759 25.10759 25.10759
BoxAngles 90 90 90
ExternalTemperature 298
ExternalPressure 101325
ComputeMoleculeProperties yes
ComputeMolecularPressure yes
ComputeMSD yes
PrintMSDEvery 5000
Movies yes
WriteMoviesEvery 100
ComputeRDF yes
writerdfevery 1000
Component 0 MoleculeName water
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
VolumeChangeProbability 0.1
CreateNumberOfMolecules 0
Component 1 MoleculeName methane
TranslationProbability 0.5
RotationProbability 0.5
CFSwapLambdaProbability 1.0
CreateNumberOfMolecules 0
WidomProbability 1.0
I included WidomProbability to compute Henry's coefficient, as described in the manual. However, the Henry's coefficient does not appear in the output. I suspect this might be due to water being a high-density liquid rather than a porous material like a MOF.
My main question is:
How can I calculate the Henry's coefficient for methane and carbon dioxide in water at varying pressures using RASPA?
This coefficient is essential for applying Henry's law to determine partial pressures for my research.
Thank you in advance for your guidance.
Best regards,
Jemilu Omeje Audu
#24
General / Seeking Advice: RASPA3 vs RASP...
Last post by wangwei - November 19, 2024, 04:23:06 AMDear everyone,
I hope this message finds you well. I am currently exploring the use of RASPA for adsorption and diffusion simulations on **CentOS 7**, and I am trying to decide between **RASPA2** and the recently released **RASPA3**.
The new RASPA3 release looks exciting, with significant speed improvements (up to 6x for benchmark systems) and additional features like thermodynamic integration, a Python API, and improved output for density computation. However, I noticed that CentOS 7 was not explicitly mentioned in the system requirements or documentation.
Given the modern C++ implementation of RASPA3, I'm concerned about potential compatibility issues with CentOS 7, which uses older libraries and compilers by default. While I can upgrade the toolchain (e.g., GCC, CMake), this would add complexity to the setup process. On the other hand, RASPA2 is more established and might be easier to get up and running on CentOS 7, though it lacks the advanced features and performance improvements of RASPA3.
**Here are my main questions:**
1. Has anyone successfully installed and run RASPA3 on CentOS 7? If so, were there any significant challenges?
2. For a CentOS 7 environment, would you recommend sticking with RASPA2 for simplicity, or is the effort to configure RASPA3 worthwhile given its new features?
3. Are there specific compatibility tips or best practices for RASPA3 on older Linux distributions?
Any guidance or shared experiences would be greatly appreciated.
Kind regards,
WANGWEI
I hope this message finds you well. I am currently exploring the use of RASPA for adsorption and diffusion simulations on **CentOS 7**, and I am trying to decide between **RASPA2** and the recently released **RASPA3**.
The new RASPA3 release looks exciting, with significant speed improvements (up to 6x for benchmark systems) and additional features like thermodynamic integration, a Python API, and improved output for density computation. However, I noticed that CentOS 7 was not explicitly mentioned in the system requirements or documentation.
Given the modern C++ implementation of RASPA3, I'm concerned about potential compatibility issues with CentOS 7, which uses older libraries and compilers by default. While I can upgrade the toolchain (e.g., GCC, CMake), this would add complexity to the setup process. On the other hand, RASPA2 is more established and might be easier to get up and running on CentOS 7, though it lacks the advanced features and performance improvements of RASPA3.
**Here are my main questions:**
1. Has anyone successfully installed and run RASPA3 on CentOS 7? If so, were there any significant challenges?
2. For a CentOS 7 environment, would you recommend sticking with RASPA2 for simplicity, or is the effort to configure RASPA3 worthwhile given its new features?
3. Are there specific compatibility tips or best practices for RASPA3 on older Linux distributions?
Any guidance or shared experiences would be greatly appreciated.
Kind regards,
WANGWEI
#25
General / Parallel computing with RASPA
Last post by kaoutarUM6P - November 13, 2024, 03:09:42 PMI am trying to run co2 adsorption on Mofs using parallelization in an HPC, I already tried running for one Mof, "in 1 node + 56 tasks + 1 cpu per task", but the running time was almost similar (few minutes difference) when using 1 cpus and 1 task (default configuration), so I would like to know if raspa does support parallelization or multi-threading ?
thank you
thank you
#26
General / Re: RASPA3 Release
Last post by youriran - October 08, 2024, 03:30:41 PMRASPA3 is currently still in the beta-phase. This means that not all functionality found in RASPA2 is already implemented and this means that bugs might still occur.
A list of features that are yet to be implemented can be found on github.
If you do find any bugs, please, report them so we can try fixing them.
Best,
Youri
A list of features that are yet to be implemented can be found on github.
If you do find any bugs, please, report them so we can try fixing them.
Best,
Youri
#27
General / RASPA3 Release
Last post by youriran - October 08, 2024, 03:27:41 PMDear everyone,
We are happy to announce the release of RASPA3. Monte Carlo with expanded ensembles are powerful methods to compute adsorption and diffusion processes in nanoporous materials. The code has been rewritten from the ground up in modern C++. Composition and value semantics allows building complex objects from simple code. Rethinking memory structures for systems and atoms drastically improves the computational efficiency of insertions and deletions.
The code shows speed ups of up to 6 times compared to RASPA2 for computing adsorption isotherms for benchmark systems, while also preserving the validity previously found in RASPA2.
Furthermore we added new features, such as fully integrated thermodynamic integration, a python API, transition-matrix Monte Carlo and improved output files for density computation. Accessibility has been improved through JSON input scripts and the python API. The code is available as binary packages through GitHub.
The new object-oriented C++ implementation allows interfacing to other codes and modular implementation of new features. Feel free to open a GitHub issue or collaborate!
The code is available via:
https://github.com/iraspa/raspa3
The accompanying paper can be found at:
JCP
Kind regards,
The RASPA3 team
We are happy to announce the release of RASPA3. Monte Carlo with expanded ensembles are powerful methods to compute adsorption and diffusion processes in nanoporous materials. The code has been rewritten from the ground up in modern C++. Composition and value semantics allows building complex objects from simple code. Rethinking memory structures for systems and atoms drastically improves the computational efficiency of insertions and deletions.
The code shows speed ups of up to 6 times compared to RASPA2 for computing adsorption isotherms for benchmark systems, while also preserving the validity previously found in RASPA2.
Furthermore we added new features, such as fully integrated thermodynamic integration, a python API, transition-matrix Monte Carlo and improved output files for density computation. Accessibility has been improved through JSON input scripts and the python API. The code is available as binary packages through GitHub.
The new object-oriented C++ implementation allows interfacing to other codes and modular implementation of new features. Feel free to open a GitHub issue or collaborate!
The code is available via:
https://github.com/iraspa/raspa3
The accompanying paper can be found at:
JCP
Kind regards,
The RASPA3 team
#28
General / Re: RxMC ensemble
Last post by dubbelda - September 30, 2024, 01:52:27 PMThey are input, you set these. These probabilities are relative to each other, and they do not influence the accuracy of the computation, just the efficiency.
#29
General / Re: Can the cavity of a MOF be...
Last post by dubbelda - September 30, 2024, 01:45:40 PMThere is a 'help' in iRASPA ('help' menu). In principle, this is about understanding the three panes in the top-left: (I) projects, (II) scenes, (III) movie frames. If you select the second tab, you can add structures to the scene.
'File' -> 'New' -> 'Objects' -> 'Ellipsoid' and then edit the properties.
'File' -> 'New' -> 'Objects' -> 'Ellipsoid' and then edit the properties.
#30
General / Re: Enthalpy of adsorption
Last post by dubbelda - September 30, 2024, 01:07:58 PMThis works in raspa3 now.
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