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Messages - Monica_Gao

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1
Output files / Shift all potential
« on: April 06, 2021, 04:24:03 PM »
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!

2
General / Warning: Reinsertion used on the charged ions
« on: December 27, 2020, 09:14:37 AM »
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

3
Input files and parameters / Re: Error in connectivity
« on: December 27, 2020, 08:46:41 AM »
Dear professor David,
Thank you very much. And Merry Chrisma  ;D

4
Input files and parameters / Re: Error in connectivity
« on: December 02, 2020, 09:30:55 AM »
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

5
Input files and parameters / Error in connectivity
« on: December 02, 2020, 09:21:04 AM »
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.

6
General / net charge warning
« on: June 18, 2020, 02:40:41 PM »
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.

7
Output files / Re: Excess adsorption
« on: April 17, 2020, 08:15:06 AM »
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!

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