I guess"Bde" is Bond dissociation energy.....First, optimize the molecule. Then break the molecule into two fragments (break the bond whose BDE you wanted to cal.) and separately do the calculation at the same level. Now use the formula "BDE = E(fragments) -E (molecule); for example, if you wanted to find out the BDE of the C-C bond in ethane, then " BDE = 2E (methyl radical) - E (ethane). You may need to perform additional calculations with larger basis sets to obtain more accurate BDE values, as there may be a chance of BSSE. If you don't know about BSSE, go through my video (th-cam.com/video/NL46plMBLic/w-d-xo.html&ab_channel=QuantumGuruJi).
@@bahire890 output file will be always a .log or .out file in Gaussian....even if it's showing that it's document 📄 file...it's because your default program to open these kind of file you have set as some text reader. Solution: open gauss view or avogadro...and then go to open menu...open that output file
@@bahire890 you might done have some mistake....that's not possible..or in extreme case it's possible only when you change the extension .out or .log to .txt .....else it's not possible
@@quantumguruji Yes, sir, when the calculation is done, I have three files: .chk, input, and output in text form. When I want to open the output file, I choose "Open with Gaussian View," and I have a .log file with uppercase letters.
The Binary Encounter Bethe (BEB) method is a computational technique used to calculate cross sections for ion-atom collisions. The method involves using a binary collision approximation, in which the collision is treated as a two-body encounter between the projectile ion and a target atom. The outcome of the collision is then described using a set of differential equations that depend on various parameters, such as the projectile energy, the impact parameter, and the atomic structure of the target. To use Gaussian output files as input for the BEB method, you will need to extract certain information from the Gaussian output file. The following steps should give you a general idea of how to do this: Perform a Gaussian calculation for the system of interest, such as an ion-atom collision at a particular energy and impact parameter. In the Gaussian output file, locate the section that contains the optimized molecular geometry for the system. This section should include the Cartesian coordinates of all atoms in the system. Extract the Cartesian coordinates of the projectile ion and the target atom from the optimized molecular geometry section. Calculate the distance between the ion and the target atom using the Cartesian coordinates. Use the distance between the ion and the target atom to calculate the impact parameter for the collision. Extract the relevant energy information from the Gaussian output file, such as the kinetic energy of the projectile ion. Use the extracted information to set up the appropriate input parameters for the BEB method, and run the calculation to obtain the desired cross section for the ion-atom collision. Note that the specific details of how to set up the input parameters for the BEB method will depend on the specific software package or code that you are using. You may need to consult the documentation or user manual for the software to determine the exact input requirements.
Sir, can you please help me to stop the shifting external coordinates during structure optimization in gaussian16. I am facing some problem with this in my system.
If you are optimizing the geometry, then for sure the coordinates will change if you are doing just a single point calculation, the coordinates remain the same. It depends on what kind of calculation you are performing. If your geometry is already optimized and you wanted to study some of its properties, then do a single-point calculation.
@@quantumguruji Thank you Sir, for reply. Actually I am simulating a protein-ligand system. I am taking ligand coordinates from proteins crystal structure PDB file, there ligand is inside the pocket. But after geometry optimization in gaussian when I am pasting these optimized coordinates in PDB file and visualising, then ligand comes out from the pocket. For optimization only internal coordinates should be changed. Why it is shifting the origin or external coordinates?
@@AnujKumar-vn2zs When you perform a geometry optimization using a program like Gaussian, the goal is to minimize the molecular system's energy by adjusting the atoms' internal coordinates. This means that the bond lengths, bond angles, and dihedral angles are modified to find a configuration with lower energy. However, the optimization process does not necessarily consider the absolute position of the molecule in space. It focuses on the relationships between the atoms. When you obtain the optimized coordinates from Gaussian and paste them back into your PDB file, you must ensure that the molecule's reference frame (origin and orientation) is maintained. Suppose the optimized coordinates you paste back into the PDB file are not appropriately aligned with the original reference frame. In that case, the ligand might appear shifted or moved from its original position. Here are a few steps you can take to address this issue: Coordinate Systems Alignment: Before pasting the optimized coordinates back into the PDB file, compare the atom positions of the ligand in the original PDB file and the optimized output. Make sure that the atom labels and order match. You may need to translate and rotate the optimized structure to align it with its original coordinate system. Use Molecular Visualization Tools: Utilize molecular visualization tools like PyMOL, VMD, or Chimera to visualize both the original and optimized PDB structures. These tools often allow you to superimpose the structures for easy comparison and alignment. Check Atom IDs and Connectivity: Ensure that the atom connectivity (bonds, angles, dihedrals) is maintained correctly after optimization. Incorrect connectivity can lead to unexpected shifts in the ligand's position. Reference Atom Selection: If your ligand has reference atoms (known not to change during the optimization), use these atoms as reference points to align the optimized structure back to the original structure. Coordinate Transformation: If necessary, perform a coordinate transformation (rotation and translation) on the optimized structure to align it with the original structure's reference frame. This transformation should be based on known reference points. Remember that geometry optimization aims to find a locally stable configuration. Still, the optimization process does not guarantee achieving the global minimum energy structure. Therefore, validating the optimized results using appropriate visualization and analysis tools is important.
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Very helpful video thank-you sir
Can you please share a video relevant to the calculations of intermediate states in organometallic reactions by using CP2K simulation package.
How to add correction while giving the input file? Kindly make a video on it.
❤
Sir plz put the dmol3 output file analysis
can you post video on how to calculate adsorption energy of a molecule on a surface. Using gaussian. i cannot find any tutorials in yt
Keep in touch for upcoming videos. Adsorption related videos are in queue. Thank you. ☺️
thanks
If I want to now the structerals parametres of molecul after optimization. can I do that?
@@TaoufikGourti everything will be there in output file.
Nice video sir 👍 How to calculate H-Bde can you please explain
I guess"Bde" is Bond dissociation energy.....First, optimize the molecule. Then break the molecule into two fragments (break the bond whose BDE you wanted to cal.) and separately do the calculation at the same level. Now use the formula "BDE = E(fragments) -E (molecule); for example, if you wanted to find out the BDE of the C-C bond in ethane, then " BDE = 2E (methyl radical) - E (ethane). You may need to perform additional calculations with larger basis sets to obtain more accurate BDE values, as there may be a chance of BSSE. If you don't know about BSSE, go through my video (th-cam.com/video/NL46plMBLic/w-d-xo.html&ab_channel=QuantumGuruJi).
@@quantumguruji Thank you sir I will try sir
hi sir i get the output file as a document text file i use a software read only.out how to convert the document text file to .out file?
@@bahire890 output file will be always a .log or .out file in Gaussian....even if it's showing that it's document 📄 file...it's because your default program to open these kind of file you have set as some text reader.
Solution: open gauss view or avogadro...and then go to open menu...open that output file
@@quantumguruji Sir, I can open it with GaussView, but the file is a text document. I want to use UCA Fukui software, which can only read .out files.
@@bahire890 you might done have some mistake....that's not possible..or in extreme case it's possible only when you change the extension .out or .log to .txt
.....else it's not possible
@@quantumguruji Yes, sir, when the calculation is done, I have three files: .chk, input, and output in text form. When I want to open the output file, I choose "Open with Gaussian View," and I have a .log file with uppercase letters.
please suggest how to use this file for binary encouter bethe method i am not able to gate nessecarry data from this output file
The Binary Encounter Bethe (BEB) method is a computational technique used to calculate cross sections for ion-atom collisions. The method involves using a binary collision approximation, in which the collision is treated as a two-body encounter between the projectile ion and a target atom. The outcome of the collision is then described using a set of differential equations that depend on various parameters, such as the projectile energy, the impact parameter, and the atomic structure of the target.
To use Gaussian output files as input for the BEB method, you will need to extract certain information from the Gaussian output file. The following steps should give you a general idea of how to do this:
Perform a Gaussian calculation for the system of interest, such as an ion-atom collision at a particular energy and impact parameter.
In the Gaussian output file, locate the section that contains the optimized molecular geometry for the system. This section should include the Cartesian coordinates of all atoms in the system.
Extract the Cartesian coordinates of the projectile ion and the target atom from the optimized molecular geometry section.
Calculate the distance between the ion and the target atom using the Cartesian coordinates.
Use the distance between the ion and the target atom to calculate the impact parameter for the collision.
Extract the relevant energy information from the Gaussian output file, such as the kinetic energy of the projectile ion.
Use the extracted information to set up the appropriate input parameters for the BEB method, and run the calculation to obtain the desired cross section for the ion-atom collision.
Note that the specific details of how to set up the input parameters for the BEB method will depend on the specific software package or code that you are using. You may need to consult the documentation or user manual for the software to determine the exact input requirements.
Sir, can you please help me to stop the shifting external coordinates during structure optimization in gaussian16. I am facing some problem with this in my system.
If you are optimizing the geometry, then for sure the coordinates will change if you are doing just a single point calculation, the coordinates remain the same. It depends on what kind of calculation you are performing. If your geometry is already optimized and you wanted to study some of its properties, then do a single-point calculation.
@@quantumguruji Thank you Sir, for reply. Actually I am simulating a protein-ligand system. I am taking ligand coordinates from proteins crystal structure PDB file, there ligand is inside the pocket. But after geometry optimization in gaussian when I am pasting these optimized coordinates in PDB file and visualising, then ligand comes out from the pocket. For optimization only internal coordinates should be changed. Why it is shifting the origin or external coordinates?
@@AnujKumar-vn2zs When you perform a geometry optimization using a program like Gaussian, the goal is to minimize the molecular system's energy by adjusting the atoms' internal coordinates. This means that the bond lengths, bond angles, and dihedral angles are modified to find a configuration with lower energy. However, the optimization process does not necessarily consider the absolute position of the molecule in space. It focuses on the relationships between the atoms.
When you obtain the optimized coordinates from Gaussian and paste them back into your PDB file, you must ensure that the molecule's reference frame (origin and orientation) is maintained. Suppose the optimized coordinates you paste back into the PDB file are not appropriately aligned with the original reference frame. In that case, the ligand might appear shifted or moved from its original position.
Here are a few steps you can take to address this issue:
Coordinate Systems Alignment: Before pasting the optimized coordinates back into the PDB file, compare the atom positions of the ligand in the original PDB file and the optimized output. Make sure that the atom labels and order match. You may need to translate and rotate the optimized structure to align it with its original coordinate system.
Use Molecular Visualization Tools: Utilize molecular visualization tools like PyMOL, VMD, or Chimera to visualize both the original and optimized PDB structures. These tools often allow you to superimpose the structures for easy comparison and alignment.
Check Atom IDs and Connectivity: Ensure that the atom connectivity (bonds, angles, dihedrals) is maintained correctly after optimization. Incorrect connectivity can lead to unexpected shifts in the ligand's position.
Reference Atom Selection: If your ligand has reference atoms (known not to change during the optimization), use these atoms as reference points to align the optimized structure back to the original structure.
Coordinate Transformation: If necessary, perform a coordinate transformation (rotation and translation) on the optimized structure to align it with the original structure's reference frame. This transformation should be based on known reference points.
Remember that geometry optimization aims to find a locally stable configuration. Still, the optimization process does not guarantee achieving the global minimum energy structure. Therefore, validating the optimized results using appropriate visualization and analysis tools is important.
@@quantumguruji Okay, many thanks to you sir.