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#1
General / Re: MOF structure atoms not sh...
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#2
General / Re: Generating Adsorbate Densi...
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#3
Input files and parameters / Identity Exchange moves in RAS...
Last post by ssharlin - January 20, 2026, 07:50:29 PMHi, I am trying to set up a simulation and want to use Identity Exchange moves. RASPA 2 included an example for this (https://github.com/numat/RASPA2/blob/master/Docs/Examples/examples.tex#L707), and the manual listed IdentityChangeProbability as an option in the Component section. I noticed it's missing from the RASPA 3 manual (https://github.com/iRASPA/RASPA3/blob/main/data/manual/raspa-manual.pdf) and from the examples. Can we no longer run simulations using Identity Exchange moves in RASPA?
#4
General / Re: Movies.pdb file issue
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#5
General / Re: Heat of adsorption calcula...
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#6
General / Movies.pdb file issue
Last post by manjusharma - November 19, 2025, 02:33:29 PMHi, 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
here is the first line from pdb file
ATOM 1 K 0 625.618 885.4532382.075 1.00 0.00 K
#7
Input files and parameters / Anisotropic volume change in B...
Last post by Amal k - November 13, 2025, 02:28:00 PMHi 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
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
#8
General / Re: MOF structure atoms not sh...
Last post by Unity - October 27, 2025, 02:53:15 PMI am encountering the same problem right now
#9
Output files / RDFs output folder in MD simul...
Last post by had-sham - October 26, 2025, 03:52:21 PMHello,
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.
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.
#10
Output files / interaction energy in output f...
Last post by had-sham - October 25, 2025, 11:50:36 AMHello 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.
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.
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