Messages

[the cif file we defined is:]

Dear Dr. David Dubbeldam

   I met something wrong when I studied the effect of flexibility of MOFs on gas separation. There was a segmentation fault occuring in my result when the pressure ranges from 0.1 bar to 10 bar.

_cell_length_a: 16.733000
_cell_length_b: 13.038000
_cell_length_c: 6.812000
_cell_length_alpha: 90.000000
_cell_length_beta: 90.000000
_cell_length_gamma: 90.000000
_symmetry_space_group_name_Hall: -I 2 2a found space group: 347
_symmetry_space_group_name_H-M: I m c m found space group: 347
_symmetry_Int_Tables_number: 343
space group found from symmetry elements: 347 (nr elements: 16)
End reading cif-file
Number of bonds: 0 0 1
Shift all potentials
Writing Crash-file!: 0
/var/spool/torque/mom_priv/jobs/794.localhost.SC: line 16: 19513 Segmentation fault      (core dumped) $RASPA_DIR/bin/simulate simulation.input


   The MOFs proposed in the study are MIL-53 series, including MIL-53(Al), MIL-53(Cr) and so on.  Refering to the example (IRMOF-1) you gave to us, I defined the information of framework. Taking MIL-53 (Cr) as example,


the cif file we defined is:

data_MIL-53ht

_audit_creation_method RASPA-1.0
_audit_creation_date 2011-3-9
_audit_author_name '?'

_citation_author_name        'C. Serre, F. Millange, C. Thouvenot, M. Nogues, G. Marsolier, D. Louer, and G. Ferey'
_citation_title              'Very large breathing effect in the first nanoporous chromium(III)-based solids: MIL-53 or Cr-III(OH).{O2C-C6H4-CO2}.{HO2C-C6H4-CO2H}(x).H2Oy'
_citation_journal_abbrev     'J. Am. Chem. Soc.'
_citation_journal_volume     124
_citation_journal_number     45
_citation_page_first         13519
_citation_page_last          13526
_citation_year               2002

_cell_length_a    16.733
_cell_length_b    13.038
_cell_length_c    6.812
_cell_angle_alpha 90
_cell_angle_beta  90
_cell_angle_gamma 90
_cell_volume      1486.14

_symmetry_cell_setting          orthorhombic
_symmetry_space_group_name_Hall '-I 2 2a'
_symmetry_space_group_name_H-M  'I m c m'
_symmetry_Int_Tables_number     74

loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'-x+1/2,y,-z'
'x+1/2,-y,-z'
'-x,-y,z'
'-x,-y,-z'
'x+1/2,-y,z'
'-x+1/2,y,z'
'x,y,-z'
'x+1/2,y+1/2,z+1/2'
'-x,y+1/2,-z+1/2'
'x,-y+1/2,-z+1/2'
'-x+1/2,-y+1/2,z+1/2'
'-x+1/2,-y+1/2,-z+1/2'
'x,-y+1/2,z+1/2'
'-x,y+1/2,z+1/2'
'x+1/2,y+1/2,-z+1/2'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z   
_atom_site_charge

Cr1      Cr     0.25000    0.75000   0.25    0.574 
O1       O      0.25000    0.686     0       -0.486
O2       O     -0.168      0.161     0.167   -0.211
C3       C     -0.033      0.032     0.179   -0.073
C2       C     -0.066      0.063     0       -0.043
C1       C     -0.137      0.132     0       0.083 
Ho1      H      0.25000    0.611     0       0.121 
H1       H     -0.060      0.058     0.329   0.035


The structure as well as the corresponding atom names are shown in the attach file, named MIL-53(Cr)ht.bmp

The flexiblity of framework was defined as follow:

#CoreShells bond  BondDipoles UreyBradley bend  inv  tors improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion
          0    5            0           0    7    0     8                3         0         0         0               0            0
#bond stretch atom n1-n2, equilibrium distance, bondforce-constant
C3 H1  HARMONIC_BOND  366001.13136396  0.95
C3 C3  HARMONIC_BOND  483413.91047488  1.36
C2 C3  HARMONIC_BOND  483413.91047488  1.36
C1 C2  HARMONIC_BOND  353750.919316375 1.42
O2 C1  HARMONIC_BOND  543840.64928424  1.25
#bond bending atom n1-n2-n3, equilibrium angle, bondforce-constant
C1 C2 C3 HARMONIC_BEND 34926.5543205787 120.0
C2 C3 H1 HARMONIC_BEND 37263.15559911 120.0
C3 C3 H1 HARMONIC_BEND 37263.15559911 120.0
C3 C2 C3 HARMONIC_BEND 90640.10821404 120.0
C3 C3 C2 HARMONIC_BEND 90640.10821404 120.0
O2 C1 O2 HARMONIC_BEND 135960.162321060 130.0
O2 C1 C2 HARMONIC_BEND 54882.4848123699 115.0
#torsion atom n1-n2-n3-n4,
O2 C1 C2  C3  TRAPPE_DIHEDRAL      0.0   0.0   1258.890391861  0.0
C1 C2 C3  H1  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C1 C2 C3  C3  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
H1 C3 C3  H1  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C2 C3 C3  H1  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C2 C3 C3  C2  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
H1 C3 C2  C3  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C3 C2 C3  C3  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
#improper torsion atom n1-n2-n3-n4,
C2 C1 O2  O2  TRAPPE_IMPROPER_DIHEDRAL 0.0 0.0   5035.561567446  0.0
C3 C2 C3  C1  TRAPPE_IMPROPER_DIHEDRAL 0.0 0.0   5035.561567446  0.0
C2 C3 C3  H1  TRAPPE_IMPROPER_DIHEDRAL 0.0 0.0   186.3157779955  0.0


There is a question here: Is it necessary to define the bond, bend, torsion information between Cr(III) and surrounding O or C? And how to obtain these information and change them into the form that RASPA can identify

The force_field_mixing_rules.def file was defined as follow:

# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
28
# type interaction
Al_      Lennard-jones      254.09      4.01
Br_      Lennard-jones      126.29      3.73
C_      Lennard-jones      52.83      3.43
Ca_      Lennard-jones      119.75      3.03
Cl_      Lennard-jones      114.21      3.52
Cr_      Lennard-jones      7.55      2.69
F_      Lennard-jones      25.16      3
Fe_      Lennard-jones      6.54      2.59
Ga_      Lennard-jones      208.81      3.9
H_      Lennard-jones      22.14      2.57
In_      Lennard-jones      301.39      3.98
N_      Lennard-jones      34.72      3.26
O_      Lennard-jones      30.19      3.12
Os_      Lennard-jones      18.62      2.78
V_      Lennard-jones      8.05      2.8
CH4_sp3        lennard-jones    148.0     3.72
CH3_sp3        lennard-jones    98     3.76
CH2_sp3        lennard-jones    46      3.96
CH_sp3         lennard-jones    17.0      4.67
C_sp3          lennard-jones     0.8      6.38
O_co2          lennard-jones    79    3.05
C_co2          lennard-jones    27.0    2.8
Ow             lennard-jones    81.9    3.16
Hw             lennard-jones    0             0
Lw            lennard-jones    0             0
S_S          lennard-jones    122     3.6
H_S         lennard-jones      50    2.5
M_S        lennard-jones       0    0
# general mixing rule for Lennard-Jones
Lorentz-Berthelot

The pseudo_atoms.def file was defined as follow:

#number of pseudo atoms
23
#type      print   as    chem  oxidation   mass        charge   polarization B-factor radii  connectivity anisotropic anisotropic-type   tinker-type
Cr1         yes     Zn     Zn     0       65.37       0.574         0           1.0     1.6      0            0          relative             0
O1          yes     O      O      0       15.9994     -0.486        0           1.0     0.68     2            0          relative             0
O2          yes     O      O      0       15.9994     -0.211        0           1.0     0.68     2            0          relative             0
C3          yes     C      C      0       12.0107     -0.073        0           1.0     0.720    0            0          relative             0
C2          yes     C      C      0       12.0107     -0.043        0           1.0     0.720    0            0          relative             0
C1          yes     C      C      0       12.0107     0.083         0           1.0     0.720    0            0          relative             0
Ho1         yes     H      H      0       1.00794     0.121         0           1.0     0.320    0            0          relative             0
H1          yes     H      H      0       1.00794     0.035         0           1.0     0.320    0            0          relative             0
He          yes     He     He     0       4.002602     0            0           1.0     1        0            0          relative             0
CH4_sp3     yes     C      C      0       16.04246     0            0           1.0     1        0            0          relative             0
CH3_sp3     yes     C      C      0       15.03452     0            0           1.0     1        0            0          relative             0
CH2_sp3     yes     C      C      0       14.02658     0            0           1.0     1        0            0          relative             0
CH_sp3      yes     C      C      0       13.01864     0            0           1.0     1        0            0          relative             0
CH2_sp2     yes     C      C      0       14.02658     0            0           1.0     1        0            0          relative             0
C_sp3       yes     C      C      0       12           0            0           1.0     1        0            0          relative             0
C_co2       yes     C      C      0       12.0107     0.7         1.508         1.0     0.720    0            0          relative             0
O_co2       yes     O      O      0       15.9994    -0.35        0.9475        1.0     0.68     0            0          relative             0
Ow          yes     O      O      0       15.9994     0             0           1.0     0.5      2            0          relative             0
Hw          yes     H      H      0       1.00794     0.524         0           1.0     1        1            0          relative             0
Lw          no      L      -      0       0           -1.048        0           1.0     1        1            0          relative             0
S_S         yes     S      S      0       32.06        0            0           1.0     1        0            0          relative             0
H_S         yes     H      H      0       1            0.21         0           1.0     1        0            0          relative             0
M_S         no      M      -      0       0            -0.42        0           1.0     1        0            0          relative             0

No extra force field defined in the force_field.def

As for the input file, we used the hybrid MCMD method to calculate the adsorption capacity of CH4 in MIL-53(Cr)

SimulationType                MonteCarlo
NumberOfCycles                100000
NumberOfInitializationCycles  100000
PrintEvery                    5000
RestartFile                   no

ContinueAfterCrash no
WriteBinaryRestartFileEvery 5000

ChargeMethod                  Ewald
Forcefield                    MIL-53-Cr-ht-pri
CutOffVDW                     12.5
RemoveAtomNumberCodeFromLabel yes

Framework             0
FrameworkName         MIL-53-Cr-ht-pri
ChargeFromChargeEquilibration yes
UnitCells             2 2 4
HeliumVoidFraction    0.5093
FrameworkDefinitions  MIL-53-Cr-ht-pri
ExternalTemperature   298.15
ExternalPressure    61000

FlexibleFramework yes

HybridMCMDMoveProbability 1.0

Movies        yes
WriteMoviesEvery 5000


Component 0 MoleculeName              CH4
            StartingBead              0           
            MoleculeDefinition        gwq_trappe   
            TranslationProbability    1.0         
            RotationProbability       1.0         
            SwapProbability           1.0         
            RegrowProbability         1.0         
            IdealGasRosenbluthWeight  1.0       
            CreateNumberOfMolecules   0           


I would be very very grateful if you can give me some suggestions.   ;D ;D ;D ;D ;D ;D

In addition, I'd like to ask you some questions:


In the first example listed in the Advanced Example, you said the adsorption of CO2 in a totally flexible IRMOF-1 using a hybrid MC and MD simulation in μVT ensemble . However, you listed another example to illustrate the CO2 adsorption in flexible IRMOF-1 in osmotic ensemble.

1. If I want to obtain the gas separation capability of a flexible MOF, which method is better for us to use? In which condition should I used the instruction of the  first example, and in which condition I should use the instruction in the second example.

2. According to Sven M. J. Rogge (Adv. Theory Simul. 2019, 2, 1800177, doi: 10.1002/adts.201800177), the hybrid MCMD is the best way to predict the adsorption behaviors in a flexible MOF in a restricted osmotic ensemble, which seems to be the combination of the first and second example (Scheme 4). In that work, he did a MD at the very beginning, but in the case of hybridMCMD method in RASPA, it seems no MD relative defination involved.  So, how does it manange to do MD simulation.
[/color]

I am really looking forward to your respond ;D ;D ;D


Sincere
Monica

Dear Prof. David.
   Can you give me some advice on the writing of def file. I create a rigid molecule like this, but when I calaculted it, it complete with nothing output, and the pbs.err file shows that shift all potential.

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
0
0
0
#Number Of Atoms
12
# Number of groups
1
# aromatic-group
rigid
# Number of atoms
12
# atomic positions
1  Ala_O1     0.868     2.37     0.463
2  Ala_C2     0.974     0.957     0.448
3  Ala_C3     -0.36     0.225     0.23
4  Ala_O4     2.109     0.435     -0.215
5  Ala_C5     -0.232   -1.292   0.413
6  Ala_N6     -0.821   0.503     -1.162
7  Ala_H7     -1.106   0.623     0.975
8  Ala_H8     -1.22     -1.8     0.244
9  Ala_H9     0.118     -1.525   1.451
10 Ala_H10   0.518     -1.674   -0.324
11 Ala_H11   -1.778   0.048     -1.29
12 Ala_H12   -0.923   1.559     -1.246
# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
               0   11            0    0            0       0        0            0         0            0         0               0            0        0            0
# Bond stretch: atom n1-n2, type, parameters
2     1     RIGID_BOND
3     2     RIGID_BOND
4     2     RIGID_BOND
5     3     RIGID_BOND
6     3     RIGID_BOND
7     3     RIGID_BOND
8     5     RIGID_BOND
9     5     RIGID_BOND
10   5     RIGID_BOND
11   6     RIGID_BOND
12   6     RIGID_BOND     
# Number of config moves
0


the information in pbs.err

read binary file
Crash set to false
read binary file
Crash set to false
_symmetry_space_group_name_H-M: P1 found space group: 1
_symmetry_Int_Tables_number: 1
space group found from symmetry elements: 1 (nr elements: 1)
_cell_length_a: 27.124000
_cell_length_b: 15.270000
_cell_length_c: 12.010000
_cell_length_alpha: 90.000000
_cell_length_beta: 94.600000
_cell_length_gamma: 90.000000
End reading cif-file
Shift all potentials


Please give me some advice on that, thank you!

Dear professor David,
   Recently, I find when I use the instruction: regrowprobability, the output result will warn that "Reinsertion used on the charged ions", but I have checked the molecular file, and there is no wrong about them. Stranger is that, the total charges of adsorbates will change with the cycle.


[Init] Current cycle: 0 out of 80000
========================================================================================================

Net charge: -4.22752e-14 (F: -4.22752e-14, A: 0, C: 0)

WARNING: REINSERTION MOVE USED ON CHARGED IONS (IF POSSIBLE, CHANGE TO RANDOM TRANSLATION MOVE TO AVOID NUMERICAL PROBLEMS)

[Init] Current cycle: 20000 out of 80000
========================================================================================================

Net charge: 1.446 (F: -4.22752e-14, A: 1.446, C: 0)

Could you please give me some advice, thank you very much!

Best regard
Monica Gao

Dear professor David,
Thank you very much. And Merry Chrisma  ;D

Dear professor David,
  I have found the mistakes in both water definition files, so if you read this problem please ignore the first question and to the second question.
  Could you please give me some advices to calculate multi-component adsorption with at least three components?
  I am very grateful and look forward to your answer.

Best regard.
Monica, Gao

Dear Professor David,
    When I calculate the Rosenbluth Weight of water in a box with a size of 30 * 30 * 30, it fails and shows "No atoms can be grown, check the connectivity of your molecule", Could you tell me how to sovle this problem? It happends in both the water defination files defined by me and the original file in RASPA.

The file defined by me:

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
647.14
22064000.0
-0.217000
# Number Of Atoms
4
# Number Of Groups
1
# H2O-group
rigid
# number of atoms
4
0 Ow      -3.0782    0.8693    0.7624
1 Hw      -3.3972    1.5074    1.4005
2 Hw     -2.1210    0.8693    0.7624
3 Lw      -3.0064    0.9436    0.8327
# 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
0 2 RIGID_BOND
# Number of config moves
0


The original file in RASPA

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
647.14
22064000.0
-0.217000
# Number Of Atoms
3
# Number Of Groups
1
# H2O-group
rigid
# number of atoms
3
0 Ow  0.8660  -0.5000   0.0000
1 Hw  1.7321  -0.0000   0.0000
2 Hw   0.0000   0.0000   0.0000       
# 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
0 2 RIGID_BOND
# Number of config moves
0

Another thing it that, some articles published in journals involves multi-component adsorption, but I tried yestaday, but it failed with an error, so could you please tell me how to work it out?

I will be very grateful if you give me some instructions and advices, thank you very much.
Best Regard,
Monica Gao.

Dear Dr. David.

   I am sure the total charge of my MOF and adsorbate are zero, but there are still show having net charge warning in my Output files, can you help me with this problem?

   Another problem is that, My adsorption condition is at ambient temperature and atmosphere pressure. and the fugacity of my adsorbate is lower than the vapor pressure, which means the partial pressure of this adsorbate is lower than its vapor pressure at atmosphere, so can you tell me why the excess adsorption is negative.

   The last but not least, can you tell me is there any good way to accelerate calculation.

   I am very grateful if you answer my questions, thank you very much.

Dear Professor David,
   I am a beginner of RAPSA, and want to ask some thing about the definition of molecule.
take C7 as an example.

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
540.13
2736000.0
0.349
# Number Of Atoms
7
# Number Of Groups
1
# Alkane-group
flexible
# number of atoms
7
# atomic positions
0 CH3_sp3
1 CH2_sp3
2 CH2_sp3
3 CH2_sp3
4 CH2_sp3
5 CH2_sp3
6 CH3_sp3
# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
               0    6            0    5            0       0        4            0         0            0         0               0            0        6            0
# Bond stretch: atom n1-n2, type, parameters
0 1 HARMONIC_BOND 96500 1.54
1 2 HARMONIC_BOND 96500 1.54
2 3 HARMONIC_BOND 96500 1.54
3 4 HARMONIC_BOND 96500 1.54
4 5 HARMONIC_BOND 96500 1.54
5 6 HARMONIC_BOND 96500 1.54
# Bond bending: atom n1-n2-n3, type, parameters
0 1 2 HARMONIC_BEND 62500 114
1 2 3 HARMONIC_BEND 62500 114
2 3 4 HARMONIC_BEND 62500 114
3 4 5 HARMONIC_BEND 62500 114
4 5 6 HARMONIC_BEND 62500 114
# Torsion n1-n2-n3-n4 type
0 1 2 3 TRAPPE_DIHEDRAL      0.0   335.03  -68.19   791.32
1 2 3 4 TRAPPE_DIHEDRAL      0.0   335.03  -68.19   791.32
2 3 4 5 TRAPPE_DIHEDRAL      0.0   335.03  -68.19   791.32
3 4 5 6 TRAPPE_DIHEDRAL      0.0   335.03  -68.19   791.32
# Intra VDW: atom n1-n2
0 4
0 5
0 6
1 5
1 6
2 6
# Number of config moves
6
# nr fixed, list
5 0 1 2 3 4
5 6 5 4 3 2
4 0 1 2 3
4 6 5 4 3
3 0 1 2
3 6 5 4

1. could you please tell me how to get the parameters of bond stretch, bond bending and especially the parameter of torsion. I think it may have a strong relation with the flexibility of this molecule.
and 2. could you please tell me how you get the critical constant of some rare substance, like ibuprofen, through experiment or some other ways?
I am looking forward your letter, thank you very much!