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Computational Chemistry - Science topic
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Questions related to Computational Chemistry
I'm looking for recommendations on software or tools that provide the most accurate and customizable 3D plotting for QSPR (Quantitative Structure-Property Relationship) models. The tool should allow for high-quality visualization of molecular descriptors and structure-property relationships, with options for customization, interactivity, and integration with computational chemistry or statistical analysis frameworks. Any suggestions on the best tools for this purpose?
I optimized the structure of Pd Acetate Trimer using HF/STO-3G and the B3LYP/LANL2DZ without any solvent. The optimization was successful without any negative frequency.
Then I added solvent IEFPCM/DCE to the system. This causes the optimization to show error link 9999. How Do I fix this problem ?
I have tried using the last optimized geometry and used that for next calculation but every time its showing same error.
I am adding the drive links to the files herewith:
It has the input geometries and log files for both without solvent and with solvent calculations.
Can anyone please help ?
I have the optimized geometry of an organic molecule and also its TD-SCF energy. The excited state wavelength predicted by Gaussian approximately matches the experimental calculations.
I have optimized the donor molecule on a model structure of pristine graphene to check whether it is binding or not. I want to find out how the UV-Vis spectrum of donor will change once it binds with graphene.
Hi Everyone,
I have some questions regarding geometry optimizations for excited states, and I hope someone can clarify them for me.
Question:
When performing calculations involving excited states in Gaussian, I should use TD-SCF methods, correct? In that case, I need to include the "td" keyword in my route line; otherwise, the calculations will be performed in the ground state.
But, specifically, for molecules with a net spin of 1, if I am interested in optimizing the geometry for T1 and T2, I should proceed as follows:
- For T1, I should change the multiplicity to 3 and not include the "td" keyword (e.g., `# opt freq L.O.T`).
- For T2, I should include "td=root=1" and set the multiplicity to 3 (e.g., `# opt freq td=(root=1) L.O.T`).
Is this specifically for molecules with a net spin of 1 because T1 is essentially their ground state on triplet?
Additionally, should all my calculations follow this route line format if I want to calculate the geometry for excited states S1, S2, S3, etc.?
- (e.g., `# opt freq td=(root=1,2,3…) L.O.T`).
Thank you!
Dear computational chemists;
I need to plot the electron density difference between the ground state and excited state using gaussian or AIMALL. I have the optimized geometry for both states.
Thank you
Hello,
I have several .xyz files (each composed of several molecules) and I'd like to find an automated way to visualize and save them.
I'd appreciate any guidance.
I am currently working on obtaining the transition state for the deprotonation of a carbocation by histidine. Initially, I froze the bond lengths between the histidine nitrogen and the proton, as well as between the proton and the methyl group being deprotonated. This approach resulted in a single imaginary frequency of over -1000 cm⁻¹ (please see the attached files: 1_input and 1_output).
I then attempted to release these constraints and recalculate the transition state. I have tried various keyword combinations, including calcfc, calcall, scf=qc, and IOP(1/8=1) in conjunction with the level of theory # opt=(ts,noeigen) freq mpw1pw91/6-31+g(d,p). However, the structure did not converge. The energy oscillates uniformly without reaching a minimum (attached is a graph showing this behavior).
Could you provide any suggestions on how to address this issue ?
Thank you for your time and assistance.

Good morning everyone,
While running fqha.x executable, the output is printed with "File containing the dos". I need phonon DOS to run fqha.x. here, I considered the phonon DOS file, which is created as one of the outputs while running matdyn.x executable. Please, let me know where am i doing wrong.
Thank you,
Dear all,
I'm trying to perform a QM/MM calculation which makes use of DLPNO-CCSD(T)-F12/D for the high level, and XBT for the low level. My input looks like this for ORCA:
!QM/XTB DLPNO-CCSD(T)-F12/D cc-pvtz-F12 cc-pvtz-F12-CABS cc-pvtz-F12-MP2fit DefGrid2 SmallPrint Opt NUMGRAD
%qmmm
QMAtoms {0:12} end
end
* xyz 0 1
coordinates for moleclues
*
I have been trying to get ORCA to run this calculation, but it keeps crashing after 3 hrs with the following error:
--------------------------------- --------------------
FINAL SINGLE POINT ENERGY (L-QM2) 0.000000000000 (Wavefunction not fully converged!)
--------------------------------- --------------------
[file orca_main/main_util_tools.cpp, line 549]: Cannot open gbw file
[file orca_main/main_util_tools.cpp, line 549]: Cannot open gbw file
However, the gbw file is there. So I was wondering what I could do to remove this error?
I want to simulate polymer in water for that I have confusion in reduce units according my understanding of reduce units if we perform simulation in reduce units means we are make a generalize model because we set sigma , Ellison, mass and other bonding parameters equal to one means we are simulating not real model.
It's like we are doing simulation of ball and spring model.
My confusion is regarding parameter that is equal to one or not for all atoms?
🚀 Introducing OpenQP: A new open-source platform for quantum chemical collaboration, now live at [OpenQP on GitHub](https://github.com/Open-Quantum-Platform/openqp). Discover innovative features like the Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory (MRSF-TDDFT) and more in our latest manuscript: [Read here](https://doi.org/10.26434/chemrxiv-2024-k846p).
👏 Kudos to incredible people: Vladimir, Konstantin, Igor, Jingbai, and many others whose dedication made this possible!
OpenQP (Open Quantum Platform) tackles sustainability and interoperability challenges in computational chemistry. The platform offers a range of autonomous modules for quantum chemical theories, including energy and gradient calculations for HF, DFT, TDDFT, SF-TDDFT, and MRSF-TDDFT, facilitating seamless integration with third-party software.
### 🔍 Key Features of OpenQP
- Autonomous modules for quantum chemistry theories, enhancing interoperability.
- Ground and excited state properties computed using [MRSF-TDDFT](https://doi.org/10.1021/acs.jpclett.3c02296).
- Nonadiabatic coupling via [TLF Technology](https://doi.org/10.1021/acs.jpclett.1c00932) using MRSF-TDDFT.
- Innovative DTCAM series [exchange-correlation functionals](https://doi.org/10.1021/acs.jctc.4c00640).
### 🚀 What’s Next?
- Spin-Orbit Coupling via [Relativistic MRSF-TDDFT](https://doi.org/10.1021/acs.jctc.2c01036).
- Ionization Potential/Electron Affinity with [EKT-MRSF-TDDFT](https://doi.org/10.1021/acs.jpclett.1c02494).

Hi all,
I'm a master student working with computational molecular fragmentation and docking.
I did a virtual screening using autodock vina of some thousends of molecules, and I'm wondering if there's a solution to fragment the molecules based on the interactions observed on the docking poses. In the end I want obtain the smiles of the fragment, the AA the fragment is interacting and the type of interaction.
Is there any methods to do this?
Hi everyone, I'm currently working on an autodock4 and I've received those warning in my running process. I don't know how to fix or how it affects to my final results. Attached below are my dpf file and cmd warning.
Thanks for your advices.


Hello dear researchers
Please I have a problem with pdos using qe
I have calculated dos, and I get it, but when I calculated pdos using projwfc.x, I got 0 values for all orbitals!!!!
I used paw pps and I don't know why this happen?
Please if someone can help me or met this problem before!?
I put some files attached here: dos.in, projwfc.in and some orbitals files (all pdos files are set to 0, you can see that all the columns are 0)!!
I'm trying to calculate the electronic energy transfer of the excited state using gaussian.
This is the command line
#p td=(singlets,nstates=6,root=1) rb3lyp/6-311g density=current eet(fragment=2)
the run keeps crash with syntax error in eet(fragment=2)
How can I solve this?
Thank you
Hello dear colleagues and professors
Please what is the recommended type of pseudopotentials for QE? ultrasoft or norm conserving??
And from where get all types of pseudos (us, nc, pbe, pbesol,......)
Tanks in advance
Hello dear colleagues and professors
Please what is the recommended type of pseudopotentials for QE? ultrasoft or norm conserving??
And from where get all types of pseudos (us, nc, pbe, pbesol,......)
Tanks in advance
Hey everyone!
I can't run any calculations on Gaussian 03 and 09. It stopped when running the l302.exe module on my new computer.
Processor: 13th Gen Intel(R) Core(TM) i9-13900HX 2.20 GHz
RAM 32.0 GB
On other computers, it runs fine with the same software.
Thank you very much!!
Hello dear researchers, I hope you are doing well.
I want to ask you a question. I have a unit cell with 24 atoms (4 A, 4 B and 16 X) and I want to substitute X atom by another atom (for example changing one X by other element).
My question is, can I substitute it within the unit cell without making supercell?? or should I make a supercell??
Hi Collegues,
To calculate entropy (T*S) and Gibbs (G) free energy of electroreductions using computational hydrogen electrode (CHE) model (according to this equation, G = E + ZPE - TS + U), can we use vaspkit after frequency calculation by VASP? I have attached some examples they mentioned on the vaspkit.
Thank you.


When I optimize the structure, there is a difference in energy with and without LORBIT tags under exactly the same conditions.
Does anyone know why there is this difference?
Hello dear researchers, I hope you are doing well.
I want to ask you a question. I have a unit cell with 24 atoms (4 A, 4 B and 16 X) and I want to substitute X atom by another atom (for example changing one X by other element).
My question is, can I substitute it within the unit cell without making supercell?? or should I make a supercell??
Hi there,
I understand one can use the mouse to click the control panel to show disulphide bonds on the protein, but just out of curiosity, is there any command line that is able to do the same, which is to show the disulphide bonds on a certain object?
I want to do NBO analysis for a molecule in the excited state [the first singlet state]. I used the following command line,
#P td rb3lyp/ 6-311g Cis=(read, root= 1) pop=nboread
but the job crash with the following error
No CIS info on Chk file
How can I solve the error??
Hello,
I run open-shell DLPNO-CCSD(T) calculations using ORCA package for some molecule-radical systems. Some systems show the T1 diagnostic value of ~0.025 which as far as I am aware, means that the systems show multiconfigurational character.
I have run stability check on the UHF reference wave function by including the
%scf stabperform true end
line in the input file
The results show that the wave function is stable. Indeed, the CCSD iteration converges slowly, taking about 75 iterations using default ORCA setting.
I use the quasi-restricted orbital for the DLPNO-CCSD(T) calculations
Is there any way to get a reliable reference wave function so that the T1 diagnostic is below 0.025?
In a groundbreaking development shared within a Facebook group, the barriers between GROMACS and Windows have been successfully dismantled. The GROMACS community is elated to announce the triumphant porting of the renowned molecular dynamics simulation software to the Windows platform. This achievement not only broadens the user base but also opens up new possibilities for collaboration and exploration in the realms of computational chemistry and bioinformatics.
Traditionally confined to Unix-based systems like Ubuntu, GROMACS has been a staple in molecular dynamics simulations. However, a recent announcement within a Facebook group has unveiled a transformative milestone – the successful porting of GROMACS to the Windows platform. This breakthrough, which allows users to run GROMACS simulations on Windows via the command prompt, signifies a significant step towards increased accessibility and inclusivity.
Installation GROMACS on Windows:
The key to this newfound accessibility lies in the GROMACS installer tailored for Windows, available for download at the following link:
This installer simplifies the process, enabling users to seamlessly integrate GROMACS into their Windows environment and execute simulations directly through the command prompt. This is installed version of Gromacs 2020.3, both CPU and GPU version is available. In GPU version, you need to install latest NVIDIA CUDA driver and in case of windows 11, you need to put a dll file in the bin folder. https://www.dll4free.com/cufft64_10.dll.html
Technical Insight:
The successful porting of GROMACS to Windows raises questions about the technical intricacies involved in this process. While the Facebook announcement doesn't delve into the specifics, the installer provided indicates a streamlined approach to bring GROMACS functionality to Windows users. Researchers and enthusiasts keen on exploring the technical aspects of this achievement are encouraged to investigate the installer and potentially contribute to the ongoing development.
Performance Evaluation:
One of the critical aspects of this porting endeavor is the performance of GROMACS on the Windows platform. Researchers are encouraged to share their experiences and insights regarding the performance of GROMACS simulations on Windows, comparing it to the traditional Unix environment. Identifying any optimizations or challenges encountered during this process will contribute to the collective knowledge of the community.
Community Collaboration:
The Facebook group announcement not only celebrates the successful porting of GROMACS to Windows but also invites the community to actively engage in the ongoing discussions. Users are encouraged to share their experiences, feedback, and potential improvements related to running GROMACS on Windows. The provided link serves as a hub for collaboration, fostering a sense of community among researchers, developers, and enthusiasts interested in GROMACS on Windows.
I am trying to calculate the NTOs of a specific td-dft calculation. I am using this input:
%oldchk=state9oh.chk
%chk=state9.chk
%nproc=8
#p m062x/6-31+G(d,p) Geom=AllCheck Guess=(Read) iop(9/40=4) Density=(Check,Transition=9) Pop=(Minimal,NTO,SaveNTO)
-3 1
--Blank line--
But, i am getting this error:
This type of calculation cannot be archived.
How can i solve it? The oldchk file is in the same folder, with the correct name.
Hello, Can anybody assist me in expanding the number of cores using gaussian 9.0 program. I have multiprocessor system with Intel® Core™ i5-1135G7 (up to 4.2 GHz with Intel® Turbo Boost Technology, 8 MB L3 cache, 4 cores) and 8GB RAM. I am using Avogadro and Gaussian, so kindly assist me where to put the commands?
I've been having some trouble with the output I've obtained from my calculations: I've tried to optimize three excited states from the same molecule. All of them reached convergence (and in all three cases the .log file states that the calculation has terminated normally). But the problem is that I can't load the .fchk file in the MO's visualization menu. When I try to do it, the following error pops up:
'SCUtil_ConnectionGFCHK::Parse_GFCHK()
Missing or bad data: MM charges
Line number: 54'
I'm fairly new to the software and to computational chemistry, sorry if it's too much of a basic question. Should I try to maybe change something manually in the .fchk file?
Hello everyone!
I'm about to start a research grant on energy storage materials. The first task is to replicate the results of a paper where they used DFT and MD calculations (with VASP) to simulate the interaction of a gas adsorbing onto a Li slab. (Stephan L. Koch, Journal of Power Sources, 2015, DOI: 10.1016/j.jpowsour.2015.07.027, Pages 150-161)
I have little experience with DFT calculations (although with Gaussian), but none with MD and VASP. Additionally, my university doesn't have a license for VASP.
Could you suggest valid alternatives to VASP and provide some teaching materials on how to use the software for these types of calculations?
Thank you very much!
From you experience, which DFT method and basis sets are recommended for organic molecules optimization using Gaussian and provide a trusted energy and proprieties ( e.g UV-vis spectra)
I have three transition states corresponding to a catalytic cycle, and there are 3 non-bonding interactions involved in them. Are there any tools available in Gaussian 16 that could quantify the strength and nature of these interactions?
Also, can Wiberg Bond order index be used for determining the above?
Dear Researchers,
There is a sentence which is frequently encountered in computational chemistry field as "this functional highly suffers from self interaction error". Could you please clarify what is the meaning of SIE and where does it originate from? Any comment is highly appreciated.
Best regards,
Saeed
[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /home/bio/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
100%|##########| 101/101 [elapsed: 08:08 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|##########| 101/101 [elapsed: 08:16 remaining: 00:00]
[INFO ] calculating ligand contribution...
100%|##########| 101/101 [elapsed: 00:02 remaining: 00:00]
[INFO ] Beginning PB calculations with /home/bio/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
0%| | 0/101 [elapsed: 00:00 remaining: ?][ERROR ] CalcError
/home/bio/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error
Check the gmx_MMPBSA.log file to report the problem.
File "/home/bio/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/bio/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.run_mmpbsa()
File "/home/bio/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/bio/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/bio/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run
GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
File "/home/bio/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
CalcError:
/home/bio/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error
Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 6.
Exiting. All files have been retained.
Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
I am calculating the oniom energy for a complex, receptor only and ligand only to calculate the free binding energy of the ligand of interest. I've seen different papers that do get similar kcal/mol calculations to their respective docking experiments but wanted an opinion on if it truly makes sense to do so. Both methods are taking in completely different things when forming their calculations. I figured each would only be able to be compared relative to each other? Example. Ligands can only be compared to each other via docking alone and ligands used in oniom can only be compared to each other through oniom.
- When to use B3LYP and CAM B3LYP? I also want to know why it is called B3LYP and CAM B3LYP?
Hello Everyone
I did a NBO calculation using %CHOOSE keylist . I used different syntax but every time I got a similar error.
"Keyword for orbital type is not LONE, BOND, or 3CBOND"
Please, Suggest me what may be possible cause of error. If it is syntax error, how it can be solved.
Thank You
In the a molecule I am working on, there is a certain O-H bond. I wanted to study the variation of energy on changing the bond length, for that I did a relax-scan computation on g16. I have generated the output where in the .log file I have 50 different structures, each with their energies.
As my next step, I want to calculate vertical excitation energy for each of the 50 structures. I can do it manually by switching to each structure from the window shown in the attachment and use the GUI to generate a .com file of energy calculation for each of them.
But this process gets too tedious and eventually impossible as the number of structures in my scan increase to >100. Is there any way to automate this using some script? Any help will be appreciated

I encountered the calculations in the research article titled " ." However, I'm having difficulty comprehending the procedure used to calculate ΔrG20 and ΔrG30, particularly when incorporating solvent model adjustments. My confusion lies in the precise method for calculating the correction terms when considering the solvent model. I've included the worksheet I employed in an attempt to replicate the results showcased in Table 3 of the mentioned article.
In Table 3 of the paper, it is stated that ΔrG20 equals −44.433 kJ/mol. Strikingly, my calculations yield a value of -26.707 kJ/mol for ΔrG20. Furthermore, for ΔrG30, the paper indicates a value of −28.424 kJ/mol, whereas my calculations result inΔrG30 = -23.355 kJ/mol. Regarding the computed redox potential (E0) using the B3LYP/6-31G(d,p) level of theory, the article reports a value of 0.682 V, but my calculations yield 0.616 V.
I would be extremely grateful for any guidance or assistance you could provide in resolving these discrepancies or any other methods (not the use of isodesmic reactions) to calculate the redox potentials of aforementioned systems using DFT calculations.
I want to determine if there are acid-base reaction or just hydrogen bond interaction between 2 organic molecules by Gaussian software. Can anyone help me on this problem? Thank you in advance.
Dear Colleagues,
I am new to the computational chemistry, and I am primarily interested in the exchange energy calculations for polynuclear metal complexes.
Is the broken-symmetry DFT approach applicable to binuclear gadolinium complexes? If so, which combination of the functional / basis set / other parameters would be appropriate to yield a convergent SCF for both HS and BS states?
How would an ORCA 5.0 input file look like for such a calculation? A routine BS-DFT calculation, which works well for copper(ii) complexes, does not yield a convergent SCF in the case of Gd(III) ions.
I want to teach computational chemistry to elementary students and I should explain this difference with basic words.
""DFT 🆚 MD""
I came across a manuscript under review titled “Neighbor List Artifacts in Molecular Dynamics Simulations”. see "Neighbor List Artifacts in Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage" This study claimed that many non-expert users rely on default values for key inputs, which can lead to deformation in some cases, such as large membranes simulations. The study also suggested that most simulations suffer from inappropriate parameters for outer cutoff, ri and nstlist, resulting in missing long-range Lennard-Jones interactions. I would appreciate any comments and suggestions.
Hello,
I am trying to run a calculation using the HF/LANL2DZ level of theory, and am interested in visualizing the canonical orbitals and the basis functions. The molecule of interest is pentagonal planar (D5h point group), and I would like to choose the coordinate system such that the py basis functions on the terminal atoms are pointing towards the center of the molecule.
Does g09 support this? What keywords would I have to add to the route section to achieve this?
Thank you very much!
Hello,
We want to continue one of our previous simulations and add one more molecule into the system. We used 53a6 force field files from ATB server for our previous simulations since we started it many years ago. However, currently, when we submit a molecule to the ATB server, it always outputs the G54A7FF force field files. Could you please tell me how can I get 53a6 files from the ATB server?
Any help would be much appreciated!
I am investigating disulfide radicals of the type in Hall et al (2014) doi:10.1021/ja500087m, and I am having trouble rationalizing the results I am getting in the optimizations using Gaussian. Obviously the lowest energy is found when the charge is symmetrically distributed, but I want to investigate the geometry and energy is the charge is localized on one sulfur. If that doesn't seem to make sense chemically, trust me I know, I'm working a hunch.
I have run a CASSCF calculation but the calculation still determines the symmetrical distribution to be better and gives that result. I have tried making one of the sulfurs a separate charged fragment and the initial guess gives me a good result, but once I run the optimization it all blends.
Is there any way to get the software to give the lowest-energy-possible-if-this-one-condition-is-met?
Thanks in advance for any ideas!
Hello, I'm a very new user of Gaussian 16. So, I started doing optimization and frequency of MIL-53(Fe) [construct with 3 atoms Fe and 4 bdc linker] cluster model using MN15L/genecp. The calculation was finished and I got inp.log. How do I know is the optimization and frequency calculation was success? And how do I get these data: (1) The optimized structure, (2) Thermodynamics (like enthalpy, Gibbs free energy, etc).
Please, advise me.
Thank you.
R. S.
This is my input
%mem=32Gb
%nproc=12
#p MN15L/genecp opt freq=NoRaman
test
-1 2
.....
****
O 0
6-31+G(d)
****
C H 0
6-31G(d)
****
Fe (lanl2ldz)
****
FE
FE-ECP (lanl2dz)
****
Note: Actually I wanna calculate the energy adsorption of CO2 using the energy that I got after opt and freq calculation with this formula: Eads= Esystem - (EMOFs + ECO2).
I'm running CHARMM36 simulations of a peptide on GROMACS and I need its N-terminus to be capped with an acetyl group. I checked the “aminoacids.n.tdb” file, but there is no entry for acetylated N-terminus. How can I find/make a terminus?
advanced technology, AI, computational chemistry, supramolecular chemistry
Can domeone advise which course, software to take to learn computational chemistry??
website as well will be appreciated
I have an allylic organic compound that I’ll be deprotonating to make an allylic anion. This anion will have the lone pair delocalizing on 2 different (chemically non equivalent) carbons. I’m trying to rationalize the regioselectivity. Which carbon will be reacting with my electrophile? And why?
I want to do a DFT calculation using Gaussian software to find out which carbon will react? Maybe by calculating the HOMO orbitals energy of the 2 different carbons each carrying the lone pair in 2 separate instances.
I’m not an expert on the subject, so any sources or references for studies conducted for examples of this sort would be appreciated.
Thanks.
I will highly appreciate if you can share one for program version 2014 or higher.
I've been having trouble with a specific library and have been considering just writing something myself as the calculation isn't so complicated (just getting the energy as a function of a reaction coordinate). As the library uses the huge vasprun.xml file to source the energy it takes quite a while to run (I'm doing the analysis locally) and am thinking about just implementing the analysis manually. Is there a good reason why I shouldn't just take the final electronic energies from the OUTCARs (or OSZICAR) along the path and plot them myself?
Also, why isn't this what the library does? Is it simply because the XML file has so much extra information so they just tend to import it so they don't need to ask the user to copy over the other VASP output files? It seems quite wasteful for my current application (changing some coordinates around some minima, doing some single-point calculations along some paths and then importing the energies).
I have a coronene molecule functionalized with hydroxyl groups. I want to calculate the charge transfer between the carbon and the OH group, using NBO. But i don't understand how can i do it.
I'm using Gaussian09, which has NBO 3.1.
I've just begun working with DFTB+ and have a set of crystal geometry optimizations completed, but I'm having trouble obtaining the crystal lattice parameters (A, B, C, Alpha, Beta, Gamma) from the output files. The detailed.out file gives the following:
Total lattice derivs
-0.000004329059 0.000013039724 0.000004783995
0.000032586726 0.000005938166 0.000006491755
0.000004334976 0.000001557498 -0.000023773308
But I haven't found anything in the manual, or any other sources on how to convert this matrix to the parameters.
Thank you for your time.
Dear Researchers,
Within the supermolecular approach, counterpoise-corrected interaction energy (not binding energy) for a simple complexation A+B--->AB is defined as:
CP-delta_E=E(complex)-E(monomer 1)-E(monomer 2) in which monomer`s geometries are taken from fully optimized geometry of complex. So, deformation energy is excluded. On the other hand, within IQA approach, total energy of a given molecular system is decomposed as E_int_total= sum(E_self)+ sum (E_int (A,B)) in which E_self indicates intra-atomic energies and E_inter(A,B) represents inter-atomic interaction of any pair atoms. Please let me know how CP-delta_E could be related to E_int_total? Or, accurately, what is the relation between these two equations term-by-term? In addition, please let me know how E_self deformation should be evaluated.
In advance, any kind attention and help is highly appreciated.
Sincerely,
Saeed
How to calculate Fermi energy level and work function for ZIF-8 MOF using Materials Studio?
I have done a mechanistic study (I am a beginner and passionate about computational chemistry) to find the reaction pathway in Jaguar Schrodinger.
It is a bulky palladium complex and reactants are also bulkier. I have used B3LYP-D3/LANL2DZ. Schrodinger gives final energy in the Gas Phase Energy (Hartree), when I am plotting the pathway through Reaction Profile Viewer it is showing energy up to 280208 kcal/mol at 298.15 K 1 atm. I think I have made some mistakes that's why the energy is going above 2 lacks. Kindly assist me.
Thank You
With 12 atoms, it run. But when I increased to 96 atoms, also increasing nbnd, ecutwfc, ecutrho, its showing error:
....
Band Structure calculation
Davidson diagonalization with overlap
c_bands: 3 eigenvalues not converged
c_bands: 2 eigenvalues not converged
c_bands: 1 eigenvalues not converged
c_bands: 3 eigenvalues not converged
c_bands: 1 eigenvalues not converged
...
After that the program stopped. The screenshot and the input file is given as attachment.

I am using TS BERNY to optimize the transition state guess structure for my sn2 reaction mechanism. However, when I proceeded to do qst3 calculation, I would receive an error link 9999 all the time. What should I do?
I am new to computational chemistry and I am trying to get the geometry optimization of TiO2 clusters specifically Ti5O10 using DFT methods and currently I am getting problems on how to converge the clusters. I tried using RHF with STO-3G basis set but the clusters are still not fully converge and it always says "The optimization did not converge but reached the maximum number of optimization cycles". Can someone help me how to converge the clusters? I've been doing this for a month now and I still don't know what is the problem.
I'm calculating the energy of all the E isomers of octadecene using Opt+Freq with DFT B3LYP 3-21G. Everything was fine from 1-octadecene to E-5-octadecene, but from E-6-octadecene onwards it wasn't able to optimize the molecule and it started turning out imaginary frequencies. I don't know what changed between 5 and 6, could it be that the hydrocarbon chain is too large to optimize? Does anyone know what could be causing thus and how to correct it? Help is very much appreciated.
Greeting,
In computational and theoretical chemistry, many basis sets are available.
- Can anyone explain the main difference between the Pople-style basis sets (3-21G, 6-31G...) and the def2 basis sets (def2-SVP, def2-TZVP...).
- What basis sets are the most efficient for the DFT optimization of metal complexes?
Any kind attention and assistance are greatly appreciated in advance.
I want to do a simulation on a cluster using mpirun. My problem is that when it runs it takes 5 minutes and it stops and gives me the following error:
"mpirun noticed that process rank 16 with PID 1524 on node cvb-10 exited on signal 9 (killed).
I should mention that the program is running up to the error point. (No problem with the simulation program).