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#91
Input files and parameters / CB/CFC Monte Carlo Input File
Last post by hooman - April 11, 2025, 06:47:04 PMDear Prof. Dubbeldam, all,
I want to simulate adsorption in MOFs using CB/CFCMC ensemble, but I'm not sure if I'm doing it the right way.
I have done it with the following settings, but although the number of cycles are relatively large and I've done a similar simulation with GCMC, I still see points in the isotherm where the uptake is not consistently increasing with partial pressure and it's at points lower than CBGCMC uptake.
Thank you very much.
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I want to simulate adsorption in MOFs using CB/CFCMC ensemble, but I'm not sure if I'm doing it the right way.
I have done it with the following settings, but although the number of cycles are relatively large and I've done a similar simulation with GCMC, I still see points in the isotherm where the uptake is not consistently increasing with partial pressure and it's at points lower than CBGCMC uptake.
Thank you very much.
You cannot view this attachment.
#92
Input files and parameters / Gibbs Ensemble Monte Carlo (GE...
Last post by hooman - April 11, 2025, 06:17:51 PMDear Prof. Dubbeldam, all,
I'm simulating adsorption in a MOF model system using the GEMC ensemble in RASPA. I have several questions regarding the methodology and input file;
1- Should the properties of the reservoir box (size, number of molecules) change in accordance to the pressure point (P as in P/Psat) in the isotherm?
2- How do I fix the volume of the MOF simulation box and how would that translate in thermodynamic terms?
3- How should I choose the proper volume move probability?
Thank you very much.
I'm simulating adsorption in a MOF model system using the GEMC ensemble in RASPA. I have several questions regarding the methodology and input file;
1- Should the properties of the reservoir box (size, number of molecules) change in accordance to the pressure point (P as in P/Psat) in the isotherm?
2- How do I fix the volume of the MOF simulation box and how would that translate in thermodynamic terms?
3- How should I choose the proper volume move probability?
Thank you very much.
#93
General / Re: Help with GCMC Simulation ...
Last post by had-sham - April 09, 2025, 11:31:46 AMHello everyone,
I reviewed the RASPA simulation output and noticed that in the input block, the density and compressibility of water are reported as 848.3 kg/m³ and 0.0000257130, which are values for the liquid phase. Since we're simulating the adsorption of water vapor, how can I resolve this issue?
Thanks!
I reviewed the RASPA simulation output and noticed that in the input block, the density and compressibility of water are reported as 848.3 kg/m³ and 0.0000257130, which are values for the liquid phase. Since we're simulating the adsorption of water vapor, how can I resolve this issue?
Thanks!
#94
General / Help with GCMC Simulation for ...
Last post by had-sham - April 06, 2025, 05:10:42 PMHi Dear RASPA Community,
I am a beginner in using RASPA and currently working on GCMC simulations for water adsorption in a MOF. I'm trying to reproduce data from the literature, where the reported water uptake at maximum relative humidity (i.e., adsorption from air) is around 30 g/g. However, in my simulation, the uptake is significantly lower—close to zero.
I have reviewed my input files multiple times but haven't been able to identify the issue. I would greatly appreciate it if someone could take a look at my simulation setup and provide guidance.
My input files are attached. For reference, the attached files are described below:
File "perfect_charge.def": The CIF file of the MOF structure. Partial charges were obtained using charge equilibration in RASPA.
File "Tip4p": The water molecule definition file.
Thank you very much for your support!
Best regards,
I am a beginner in using RASPA and currently working on GCMC simulations for water adsorption in a MOF. I'm trying to reproduce data from the literature, where the reported water uptake at maximum relative humidity (i.e., adsorption from air) is around 30 g/g. However, in my simulation, the uptake is significantly lower—close to zero.
I have reviewed my input files multiple times but haven't been able to identify the issue. I would greatly appreciate it if someone could take a look at my simulation setup and provide guidance.
My input files are attached. For reference, the attached files are described below:
File "perfect_charge.def": The CIF file of the MOF structure. Partial charges were obtained using charge equilibration in RASPA.
File "Tip4p": The water molecule definition file.
Thank you very much for your support!
Best regards,
#95
Input files and parameters / Question about Gibbs simulatio...
Last post by Kimchen - March 20, 2025, 12:32:28 PMHallo everyone, i got an error message of:WARNING: ENERGY DRIFT (INTERNAL CONSISTENCY ERROR IN THE CODE), THE SIMULATION RESULTS ARE WRONG!! in Gibbe ensemble simulation of H2.
Here is my parameters:
force field mixing
# general rule for shifted vs truncated
truncated
# general rule tailcorrections
yes
# number of defined interactions
2
# type interaction, parameters. IMPORTANT: define shortest matches first, so that more specific ones overwrites these
H_h2 none //
H_com FEYNMAN HIBBS LENNARD JONES 36.7 2.958 // idem
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
pseudo_atom:
#number of pseudo atoms
2
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type 0
H_h2 yes H H 0 0.0 0.468 0.0 1.0 0.31 0 0 relative 0
H_com no H - 0 2.016 -0.936 0.0 1.0 0.31 0 0 relative 0
H2.def:
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
33.19
1293000.0
-0.22
# Number Of Atoms
3
# Number Of Groups
1
# H2-group
rigid
# number of atoms
3
# atomic positions
0 H_h2 0.0 0.0 0.37
1 H_com 0.0 0.0 0.0
2 H_h2 0.0 0.0 -0.37
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
# Number of config moves
0
Does anyone know whats the problem?
Here is my parameters:
force field mixing
# general rule for shifted vs truncated
truncated
# general rule tailcorrections
yes
# number of defined interactions
2
# type interaction, parameters. IMPORTANT: define shortest matches first, so that more specific ones overwrites these
H_h2 none //
H_com FEYNMAN HIBBS LENNARD JONES 36.7 2.958 // idem
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
pseudo_atom:
#number of pseudo atoms
2
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type 0
H_h2 yes H H 0 0.0 0.468 0.0 1.0 0.31 0 0 relative 0
H_com no H - 0 2.016 -0.936 0.0 1.0 0.31 0 0 relative 0
H2.def:
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
33.19
1293000.0
-0.22
# Number Of Atoms
3
# Number Of Groups
1
# H2-group
rigid
# number of atoms
3
# atomic positions
0 H_h2 0.0 0.0 0.37
1 H_com 0.0 0.0 0.0
2 H_h2 0.0 0.0 -0.37
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
# Number of config moves
0
Does anyone know whats the problem?
#96
General / What is the source of GenericM...
Last post by Sipra Mohapatra - March 13, 2025, 06:47:54 AMHii all,
Is GenericMOF FF safe for MOF simulations? I am not finding any citation for the force field. Is it the modified version of UFF/Dreiding? Can someone explain?
Is GenericMOF FF safe for MOF simulations? I am not finding any citation for the force field. Is it the modified version of UFF/Dreiding? Can someone explain?
#97
Announcements / Re: RASPA workshop announced (...
Last post by Sipra Mohapatra - March 12, 2025, 04:41:16 PMIs there a possibility of a RASPA workshop being held in 2025?
#98
Input files and parameters / Ethylene with TraPPe UA2 probl...
Last post by CheMiNuB - March 08, 2025, 10:38:21 PMIm trying to simulate the adsorption of c2h4 on mofs using different models
only with TraPPe_UA2 i keep getting the error
Simulation finished, 1 warnings
WARNING: ENERGY DRIFT (INTERNAL CONSISTENCY ERROR IN THE CODE), THE SIMULATION RESULTS ARE WRONG!!
Here's my Model
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
282.4
5032000.0
0.085
# Number Of Atoms
4
# Number Of Groups
1
# Alkane-group
Rigid
# number of atoms
4
# atomic positions
0 CH2_sp2 0.0 0.0 0.0
1 CH2_sp2 1.70 0.0 0.0
2 D 0.85 0.65 0.0
3 D 0.85 -0.65 0.0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
2 3 RIGID_BOND
# Number of config moves
0
Anybody has any ideas ?
only with TraPPe_UA2 i keep getting the error
Simulation finished, 1 warnings
WARNING: ENERGY DRIFT (INTERNAL CONSISTENCY ERROR IN THE CODE), THE SIMULATION RESULTS ARE WRONG!!
Here's my Model
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
282.4
5032000.0
0.085
# Number Of Atoms
4
# Number Of Groups
1
# Alkane-group
Rigid
# number of atoms
4
# atomic positions
0 CH2_sp2 0.0 0.0 0.0
1 CH2_sp2 1.70 0.0 0.0
2 D 0.85 0.65 0.0
3 D 0.85 -0.65 0.0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
2 3 RIGID_BOND
# Number of config moves
0
Anybody has any ideas ?
#99
Input files and parameters / I need help running MC simulat...
Last post by Ismail - March 04, 2025, 03:18:04 PMDear Professors,
I am a beginner with RASPA. And i am running a project on atmospheric water adsorption using COFs. I am facing errors of PseudoAtomNumber. I have tried all my best to resolve this issue but i am not getting it. Please help.
My files are attached for your reference.
Thank you and i look forward to your suggestions
I am a beginner with RASPA. And i am running a project on atmospheric water adsorption using COFs. I am facing errors of PseudoAtomNumber. I have tried all my best to resolve this issue but i am not getting it. Please help.
My files are attached for your reference.
Thank you and i look forward to your suggestions
#100
General / Re: Question about raspa
Last post by David Dubbeldam - February 26, 2025, 03:52:26 PMYes, rigid molecules are supported. Also, per component you can block or allow certain regions for insertion/deletion.
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