Recent posts

#1

General / Movies.pdb file issue

Last post by manjusharma - November 19, 2025, 02:33:29 PM

Hi, while writing movies.pdb file for cationic zeolites, coordinates for cations are written as very large numbers, kindly help.

here is the first line from pdb file

ATOM      1 K            0     625.618 885.4532382.075  1.00  0.00           K

#2

Input files and parameters / Anisotropic volume change in B...

Last post by Amal k - November 13, 2025, 02:28:00 PM

Hi all,
I am working on a system of Gas-Hydrates. I have a few questions regarding the nature of the input files. I hope one of you can help me figure it out.

I wanted to perform a MuPT simulation on a system consisting of a hydrate system and a vacuum in one direction, with some molecules adsorbed within it. I performed a MuVT at the beginning using the RestartInitial file, where the additional vacuum in the x direction was created by editing the box length in the restart file; the adsorbates were then properly inserted. Now, when trying to perform MuPT from the MuVT's final configuration, it appears that for the box definition, you can't perform an anisotropic change, such as only along the x-axis, the direction along which I created the vacuum during MUvT. The y and Z directions should retain the box length. Surprisingly, when using MuPT with a flexible framework, the isotropic volume move was accepted. So I converted them to CIF, but now RASPA won't recognise the adsorbed atoms (the ones I got from initial MuVT) as adsorbate, but they are recognised as framework, and as a result, the number of adsorbate won't change ( I guess this happens because MuVT doesn't focus on framework atoms). The queries are

1) Is there any way I can specify the coordinates of adsorbates in CIF( Framework definition) and still get them printed in the 0th cycle? so that it won't be considered as a framework. I think naming them as cations doesn't work, as you can't give coordinates of cations in CIF. If I give a CreateNumber of adsorbates, it creates more adsorbates than the ones I need from CIF.
2) If I can somehow make isotropic volume change work for the BOX definition initialised from RestartInitial, then these problems are all solved. So, is there any way an anisotropic volume change can be done for the Box definition? I even tried the Box shape change, but it didn't work. Maybe I tried it wrong. As I am pretty stuck with this, any sort of insights is highly appreciated

#3

General / Re: MOF structure atoms not sh...

Last post by Unity - October 27, 2025, 02:53:15 PM

I am encountering the same problem right now

#4

Output files / RDFs output folder in MD simul...

Last post by had-sham - October 26, 2025, 03:52:21 PM

Hello,
When running molecular dynamics simulations, are the radial distribution function (RDF) results averaged over all frames from the entire production trajectory, or do they only represent the final configuration?

I want to know if the RDF outputs give me time-averaged structural information or just a single snapshot at the end of the simulation.

Thank you for clarifying.

#5

Output files / interaction energy in output f...

Last post by had-sham - October 25, 2025, 11:50:36 AM

Hello to everyone,

In the RASPA output file, the interaction energies (like host-guest and guest-guest) are given in units of Kelvin (K).

After I convert these energies to kJ/mol, what does the "per mol" refer to?

Is it per mole of unit cells?

Per mole of supercells?

Per mole of the entire system (adsorbent + adsorbate)?

Or per mole of adsorbate molecules?

Thank you for your help.

#6

Output files / Re: ENERGY DRIFT

Last post by cmoralesd - October 24, 2025, 07:57:24 PM

I'm having the same problem. How do I set the hard sphere potential?

In the force_field_mixinxing_rules.def you define your hard sphere potential for the desired atom type. Here a minimal example

Code Select Expand

# general rule for shifted vs truncated
truncated
# general rule tailcorrections
yes
# number of defined interactions
1
# type,        interaction,                   sigma [A]
H_CH           hard-sphere                    1.000   


#7

Output files / Re: ENERGY DRIFT

Last post by Martin li - September 24, 2025, 02:38:07 AM

I'm having the same problem. How do I set the hard sphere potential?

#8

General / Inquiry About Warning in Adsor...

Last post by Martin li - September 20, 2025, 07:12:39 AM

Dear raspa Team,

I recently performed a GCMC simulation to study the adsorption of CO₂ in a porous material under ambient temperature and pressure (100 kPa). While analyzing the results, I encountered a warning regarding the adsorption enthalpy calculation.

I would like to understand the possible reasons for this warning and seek your guidance on how to address it.

Thank you for your time and assistance. I greatly appreciate your support and expertise in helping me resolve this matter.

Looking forward to your response.
[attach id=138 width=10 height=10]1.png
Best regards,
Martin

#9

General / Query for Ruptura Manual

Last post by K_A - August 20, 2025, 03:25:51 PM

Hi Ruptura Team,

I am new to ruptura and have been trying to make it work.I will be grateful if someone can explain what does the following lines mean in the handout. 


ColumnPressure [int]
The index of the column in the raw-data file containing
the information on the pressure.


In addition, what is the physical meaning of 'Number of adsorption sites' in the code?

Regards.
Khadija
khadija.asif@strath.ac.uk

#10

General / RASPA3-COMPILATION ERRORS

Last post by K_A - August 13, 2025, 02:51:06 PM

Hi Raspa Team,

I am trying to compile the code but it keeps on giving me this error. I have tried building it with both CONDA and ninja, these similar errors keep popping up.

1 error generated.
[552/4649] Building CXX object src/CMakeFiles/raspakit.dir/foundationkit/hdf5.ixx.o
FAILED: src/CMakeFiles/raspakit.dir/foundationkit/hdf5.ixx.o src/CMakeFiles/raspakit.dir/hdf5.pcm

I shall be grateful if someone can help me resolve this or can advise.

Thankyou.
Regards.