Recent posts

#41

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

#42

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?

#43

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?

#44

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

#45

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).

#46

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.

#47

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.

#48

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.

#49

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.

#50

Simulation algorithms and theory / Re: MaxNumberOfCoulombicSites

Last post by AntonioDouglas - December 22, 2024, 08:02:51 AM

Hello everyone!
I am having the same problem when trying to use RASPA 2.0.47. At the time, I am running calculations in a highthroughput screening scheme. However, only a part of the .cif files that constitute the group of structures I am studying are calculated. The other structures fall into a loop that returns the following calculation status in a slurm file:
"
[...]
unknown: 1,000
unknown: 1,000
unknown: 1,000
End reading cif-file
Shift all potentials
'force_field.def' file not found and therefore not used
Realloc MaxNumberOfCoulombicSites: 2048
realloc(): invalid next size
_cell_length_a: 7.119000
_cell_length_b: 21.580000
_cell_length_c: 9.100000
_cell_length_alpha: 90.000000
_cell_length_beta: 90.000000
_cell_length_gamma: 90.000000
_symmetry_space_group_name_H-M: P 1 found space group: 1
_symmetry_Int_Tables_number: 1
space group found from symmetry elements: 1 (nr elements: 1)
unknown: 1,000
unknown: 1,000
[...]
unknown: 1,000
unknown: 1,000
unknown: 1,000
End reading cif-file
Shift all potentials
'force_field.def' file not found and therefore not used
free(): invalid pointer
Realloc MaxNumberOfCoulombicSites: 2048
realloc(): invalid next size
free(): invalid pointer
Realloc MaxNumberOfCoulombicSites: 2048
realloc(): invalid next size
free(): invalid pointer
free(): invalid pointer
Realloc MaxNumberOfCoulombicSites: 2048
realloc(): invalid next size
free(): invalid pointer
"
And then the calculation crashes in an abnormal termination.

I am a beginner with RASPA. I looked in the manual, chapter 5 "the source code" and found no mention of the part of the code that deals with the subject raised (MaxNumberOfCoulombicSites).

Can you tell me where, in which file contained in the /src/ folder I can find the code, and what is the best way to modify it so that I can overcome this problem?

Thank you in advance, thank you very much.