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#1
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?
#2
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?
#3
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?
#4
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 ?
#5
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
#6
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.
#7
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.
#8
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!
#9
General / No general mixing rule but I s...
Last post by Jacker - February 16, 2025, 03:51:12 PMHi Dr Dubbeldam:
I am a new user to the RASPA2.0.
I have run the examples from the RASPA2.0 manual and my own tests, warning of atom-pairs with no VDW interactions have been found in the output files.
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!
Best
Jacker
I am a new user to the RASPA2.0.
I have run the examples from the RASPA2.0 manual and my own tests, warning of atom-pairs with no VDW interactions have been found in the output files.
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!
Best
Jacker
#10
General / Question about raspa
Last post by antoine - February 10, 2025, 02:16:11 PMHello everyone, I hope you are doing well. I want to start using RASPA for GCMC simulations and would like to know if RASPA supports defining specific regions for insertion, deletion, and Monte Carlo moves. Additionally, does it support rigid molecules, such as the SPC water model in my case?
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