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#1
Input files and parameters / Re: No VDW interaction
Last post by Jacker - Today at 12:02:15 PM
Have you addressed the above issues? I am experiencing the same problem, please give me some suggestions on how to solve this problem.
I am using RASPA2 to simulate the adsorption of CH4 on Aragonite (CaCO3) using UFF-Dreiding force field and methane molecule, and the results keep showing THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION C-O C-Ca C-CH4_sp3 Ca-C Ca-O Ca-CH4_sp3 CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-C (maximum interactions shown).sp3 O-C O-Ca O-CH4_sp3 Ca-C Ca-O Ca-CH4_sp3 CH4_sp3-C CH4_sp3-O CH4_sp3-Ca (maximum 50 interactions shown); I set to general mixing rule for Lennard-Jones: Lorentz-Berthelot, but the result is "No general mixing rule: all cross term specified individualy",I have not found the reason for this, how to remove this warning, please advise me, thank you!
#2
General / No general mixing rule but I s...
Last post by Jacker - February 16, 2025, 03:51:12 PM
Hi Dr Dubbeldam:

I am a new user to the RASPA2.0.
I have run the examples from the RASPA2.0 manual and my own tests, warning of atom-pairs with no VDW interactions have been found in the output files.

I am using RASPA2 to simulate the adsorption of CH4 on Aragonite (CaCO3) using UFF-Dreiding force field and methane molecule, and the results keep showing THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION C-O C-Ca C-CH4_sp3 Ca-C Ca-O Ca-CH4_sp3 CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-C (maximum interactions shown).sp3 O-C O-Ca O-CH4_sp3 Ca-C Ca-O Ca-CH4_sp3 CH4_sp3-C CH4_sp3-O CH4_sp3-Ca (maximum 50 interactions shown); I set to general mixing rule for Lennard-Jones: Lorentz-Berthelot, but the result is "No general mixing rule: all cross term specified individualy",I have not found the reason for this, how to remove this warning, please advise me, thank you!

Best

Jacker
#3
General / Question about raspa
Last post by antoine - February 10, 2025, 02:16:11 PM
Hello everyone, I hope you are doing well. I want to start using RASPA for GCMC simulations and would like to know if RASPA supports defining specific regions for insertion, deletion, and Monte Carlo moves. Additionally, does it support rigid molecules, such as the SPC water model in my case?
#4
General / Limit on the number of atoms
Last post by cvm14 - February 10, 2025, 05:10:03 AM
Dear Professor,

I have a system with more than 100 atoms, including heavy atoms and a transition metal, along with C, H, and O. I want to perform density estimation using an NPT ensemble in RASPA. When I attempted this calculation, it returned no output directories or error messages. I wonder if RASPA allows a certain number of atoms during execution, as I could run a molecule with the same elements as above but with less than 100 atoms. Can you please direct me on how to tackle this issue?

#5
General / Re: Seeking Advice: RASPA3 vs ...
Last post by David Dubbeldam - January 29, 2025, 10:23:51 PM
There are packages for linux, including centos 7 at:
https://github.com/iRASPA/RASPA3/releases
#6
Visualization / Re: Adsorption density distrib...
Last post by David Dubbeldam - January 29, 2025, 07:31:14 PM
You probably used "surface"-rendering. With "volume-rendering" you can get more of a color-gradient.
Bonding is controlled by a general rule, also employed by VMD: The radius < (covalent radius of atom1 + atom2 + 0.56).
#7
General / Re: Parallel computing with RA...
Last post by David Dubbeldam - January 29, 2025, 07:25:12 PM
No, RASPA does not use parallelism. But, for example, usually each point in an isotherm is computed separately and you can use an "embarrassingly parallel" approach.
#8
General / Re: Monte carlo on biomolecule...
Last post by David Dubbeldam - January 29, 2025, 07:23:07 PM
No, that is not possible. Usually docking software is used for that. I would look into 'gromacs' for biomolecules as a start.
#9
General / Re: Macromolecules
Last post by David Dubbeldam - January 29, 2025, 07:21:21 PM
In principle there is no limit. But Monte Carlo is limited to small molecules, usually molecules of 1-20 atoms. 30 atoms is already considered very, very large.
#10
General / Re: Force field issue ?
Last post by David Dubbeldam - January 29, 2025, 07:19:33 PM
That is what makes classical simulations more difficult than quantum. But for many systems, forcefields have been published in the literature.
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