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#31
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!
#32
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,
#33
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?
#34
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?
#35
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?
#36
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 ?
#37
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
#38
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.
#39
General / Re: No general mixing rule but...
Last post by David Dubbeldam - February 26, 2025, 03:47:11 PMYou have not specified the interactions for 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 etc. Generally you will need to define these in the 'force_field_mixing_rules.def' file, using a self-interaction and a mixing rule to get the cross-interactions.
#40
Input files and parameters / Re: No VDW interaction
Last post by Jacker - February 18, 2025, 12:02:15 PMHave you addressed the above issues? I am experiencing the same problem, please give me some suggestions on how to solve this problem.
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!
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!
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