Recent posts

#1

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

#2

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).

#3

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.

#4

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.

#5

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.

#6

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.

#7

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.

#8

General / Force field issue ?

Last post by ibnalsham - December 18, 2024, 11:20:36 PM

how do I know which force field to use ?

#9

General / Macromolecules

Last post by mms - December 09, 2024, 07:29:04 AM

Hi Professor,

Is there a maximum number of atoms in the molecule.def? I have a macromolecule that has more than 1000 atoms and it is giving me a segmentation fault error

#10

Input files and parameters / Re: Crash restart

Last post by trannghia207 - December 05, 2024, 06:20:53 AM

I 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.