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1
General / Re: Problems installing on Ubuntu
« Last post by heitorabreu on April 08, 2021, 09:25:16 PM »
Now it is working fine.
Thank you!
Heitor
2
General / Re: Problems installing on Ubuntu
« Last post by David Dubbeldam on April 08, 2021, 04:19:10 PM »
Apparently, the new Ubuntu removed sysctl. I have replaced sysctl by uctsname.
Please update to v2.0.42, and check whether it now works for you on Ubuntu 20.10.
3
Visualization / Re: Get channel and cages from zeolites in iRaspa
« Last post by David Dubbeldam on April 08, 2021, 10:00:31 AM »
Drag the MFI-example to your local projects so that it is editable. Then select the channel in the 'Scene Navigator' (See help).
After that go to the detail-view called 'Appearance' on the right, and set the properties of the 'primitive' (like the color and shape/size of the cylinder primitive).
4
General / Problems installing on Ubuntu
« Last post by heitorabreu on April 08, 2021, 03:37:00 AM »
Dear all,
I am trying to install RASPA on ubuntu 20.10 and I am having the following problem:

output.c:43:10: fatal error: sysctl.h: Arquivo ou diretório inexistente
   43 | #include <sysctl.h>

Can anyone help me with this problem?

Thank you in advance.
5
Output files / Shift all potential
« Last post by Monica_Gao 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!
6
Visualization / Re: Get channel and cages from zeolites in iRaspa
« Last post by cbornes on March 31, 2021, 10:25:08 AM »
Dear David

Thanks for the answer, I was wondering if there is a way to indicate the channel intersections in a different way showing they are bigger. I remember zeomics allowed to make the channels in yellow and the channel intersections in blue and it was easy to see that they were much larger. But I guess Zeomics does not work nowadays and it's way less flexible than iRaspa.

Also, how can I do this channel representation for other zeolites?

Thanks
7
Visualization / Re: Get channel and cages from zeolites in iRaspa
« Last post by David Dubbeldam on March 25, 2021, 03:13:45 PM »
It is a standard example of iRASPA. It is in the gallery examples.
Gallery -> Primitives -> MFI
8
Visualization / Get channel and cages from zeolites in iRaspa
« Last post by cbornes on March 23, 2021, 08:38:43 PM »
Hi

I'm trying to get a similar image to the one linked below. I'm want to get a schematic representation of the channel system of MFI.

Also is it possible to get the channel intersections?

https://www.compchem.nl/wp-content/uploads/MFI-schematics-1536x864.png
9
General / Slit pore/ visualization/adsorption
« Last post by isaaraujo on March 17, 2021, 06:43:58 AM »
Dear Dr Dubbeldam,

I am simulating in RASPA adsorption of methane on an illite surface. I am using pyrophyllite (Al2Si4O10(OH)2) as my framework (neutral clay) and considering isomorphic substitution (one silica atom in tetrahedral layers is replaced by an aluminum atom so that the clay sheet has a negative charge). The negative charge is neutralized by potassium, therefore K ( potassium) is a cation component.
I have three questions:

1) I would like to perform my adsorption simulations on an illite slit pore. For instance, I would like to have two clay sheets separated by a fixed distance. Is it possible to make a slit pore on RASPA? If yes, are there any explanation or examples in the manual?

2) I am running the adsorption simulations but I don't see a way to visualize the final system: framework + cations + adsorbate together. In movies/System I can only see the framework without the cations. How can I  have a picture or a .pdb file of my final system (framework + cations + adsorbate  together)?

3) Is there any reason why RASPA would give zero absolute adsorption ?

Thank you.

My simulation input:
___________________________________________________
SimulationType                MonteCarlo
NumberOfCycles                25000
NumberOfInitializationCycles  100000
PrintEvery                    1000

ContinueAfterCrash            no
WriteBinaryRestartFileEvery   2000

Forcefield                    CLAYFF
CutOffVDW                     12.5
RemoveAtomNumberCodeFromLabel yes

RandomlySubstitute 1 Si1 Al

Framework 0
FrameworkName illite
UnitCells 5 3 1
HeliumVoidFraction 0.64
ExternalTemperature 300.0
ExternalPressure 1e4 1e5

ComputeNumber1fMoleculesHistogram yes
WriteNumberOfMoleculesHistogramEvery 5000
NumberOfMoleculesHistogramSize 1100
NumberOfMoleculesRange 80

ComputeEnergyHistogram yes
WriteEnergyHistogramEvery 5000
EnergyHistogramSize 400
EnergyHistogramLowerLimit -110000
EnergyHistogramUpperLimit -20000

Component 0 MoleculeName                 kalium
       MoleculeDefinition           Cations
       TranslationProbability       1.0
       RandomTranslationProbability 1.0
       ExtraFrameworkMolecule       yes
       CreateNumberOfMolecules      15

Component 1 MoleculeName             methane
            MoleculeDefinition       TraPPE
            TranslationProbability   0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0

Thank you.
Isa
10
Output files / Abnormal atoms position output when Stiffness is smaller than 1
« Last post by Haolong on March 13, 2021, 01:30:58 PM »
 Dear Dubbeldam,

There is abnormal position output for atoms in the molecule with extremely low stiffness(1e-20), which is shown as below:

ATOM      1  O   MOL            24.547   0.074   0.871  1.00  0.00           O 
ATOM      2  H   MOL            24.330  -0.629   1.483  1.00  0.00           H 
ATOM      3  H   MOL            24.677  -0.370   0.033  1.00  0.00           H 
ATOM      4  O   MOL            28.454  26.114   3.621  1.00  0.00           O 
ATOM      5  H   MOL            28.578  25.307   4.121  1.00  0.00           H 
ATOM      6  H   MOL            29.160  26.107   2.976  1.00  0.00           H 
ATOM      7  K   MOL          -54312228503.48764424509490.218-8260815321.219  1.00  0.00           K 
ATOM      8 Cl   MOL          59751111813.535-73398710417.3009088062024.881  1.00  0.00          Cl 
ATOM      9  K   MOL          -7045318285.63313304773408.7447403388878.031  1.00  0.00           K 
ATOM     10 Cl   MOL          7750843838.857-14637127284.649-8144771966.366  1.00  0.00          Cl 

The reason why I set the stiffness as 1e-20 is that I want to insert the K and CL ions in pairs and make sure these ions can be distributed freely in the system to simulate the condense system with water molecules and ions, at the meantime, maintain the electric neutrality.

However, it turns out that when the stiffness is lower than 1,e.g: 1e-5,1e-10 and 1e-15, the output of the ions' position becomes higher than the box length of the system.

At first, I think that's because of the wrap-up issue, so I wrap those coordinates up by the length of the box, but the ions aggregate on one side and even overlap with each other, which is shown in the attachment.

Could you please tell me: 1. Can I set the stiffness lower than 1 in RASPA?
                                     2. How can I wrap up properly in this situation?

Thanks a lot!

Kind regards
Haolong

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