Tag: comp_chem

Hello! I wanted to ask for some advice about how to manage and balance job opportunities when they come in. Not to humblebrag, but I’ve been offered a genuinely great postdoc opportunity where I’m certain I’d learn a lot with a potential to visit the lab in person soon. I…

Hi! I’m a chemistry undergrad. For my research, I performed docking using Autodock Vina. For further validation, I tried docking using SwissDock too. But now, the two programs give different results. They predict different ligands to give the most favorable binding. I read that Autodock is more reliable. So, should…

Hi r/comp_chem I am attempting to calculate the for several hydrogen abstraction steps using different heteroatoms on a doublet surface in Gaussian09. When look at the Gibbs energy energy difference between the separated species and the TS I get a positive barrier, but when I look at the enthalpy difference…

Hello, I just have a little question. I performed a scan on a molecule using ORCA, and structurally, I got what I was looking for using avogadro to display. The energies it displays look promising, but I’d like to be able to see what the structure of the molecule is…

I am an undergraduate who’ll graduate in 2 years. I think I want to get a PhD in computational chemistry (although not sure where, might want to study in the US), and I’ve had around 5 months of research experience in computational chemistry in an research internship. However, I’ve only…

I ran some REMD calculations with GROMACS and wish to create a plot which depicts the free energies of the different regions on the Ramachandran plot of my protein at a specific temperature, similar to figure 2 in the following paper below. Article Antifreeze Glycoproteins Bind Reversibly to Ice via…

Hi,I am working with CREST/xtb to do some conformer searches. Been reading the docs to understand how to configure the environmental variables. I want to adjust them to suit my system (24 threads workstation) but not sure what to adjust. Wondering if someone can assist in explaining these with simpler…

Hello again! I am calculating a reaction pathway that involves diradical intermediates. One of the intermediates is a nitrene diradical, and at the CASSCF level it is described by a single determinant with the these two singly-occupied orbitals:imgur.com/C0eC7F6 What is the difference between such a diradical wavefunction and a singlet…

Hello everyone, I recently ran some docking experiments in Maestro at a university computer. The problem is that I cannot be at that computer all the time. Is it possible to open the data in, for example, PyMOL so I can work on my personal computer? And if so, would…

I am an undergraduate researching in a computational chem lab at UMD. I am done running many HMMM and then AA simulations via CHARMM and NAMD. So far HMMM simulations were converted to AA when the secondary structure seemed stable and the distance to the bilayer was minimal through visual…

Hi, I have a dataset of currently roughly 1500 reaction barriers (one reaction partner is constant) and growing. I thought it might be fun to see if we can predict barrier heights from the structure of the changing reactant. Anyone knows any papers that include their code where we could…

Hello everyone, I am trying to model the deposition of a polyelectrolyte on a glass surface to find the time it takes to fully coat the surface. This deposition is based on the difference of charge between the polyelectrolyte and the glass surface. I have created the water model and…

It seems like most comp chemists lie on the spectrum in terms of their research application, which spreads from biochemical (proteins, drug design, biomolecular simulations, etc.) to inorganic materials (semiconductors, minerals/crystals, battery/electrolytes, alloys, metals, etc.). I think it’s a notable spectrum because these fields have entirely different software suites dedicated…

I’m about to get my PhD in computational chemistry from Stanford. My thesis involved machine learning to make accurate force fields, mainly for materials science applications. But I have some experience with biology as well. I’ve been interviewing for comp chem/research jobs and I’m looking for advice in case others…

I want to relax an interface using SIESTA with a method similar to ISIF = 2 in VASP. However, SIESTA has the following options for relaxation, MD.VariableCell = which is analogous to ISIF = 3 in VASP, Constant.Volume = which is analogous to ISIF = 4 in VASP and MD.RelaxCellOnly…

I’m a second year phd student running mostly orca calculations on a range of MOFs and quantifying their properties (mostly reaction free energies of adsorption for small molecules). However, from next year I’ll be running some MD simulations to track diffusion of ions through MOF pores. I’m already familiar with…

Hi! I am doing my first docking study for my undergraduate research. And I have not been able to proceed beyond running AutoGrid. I keep getting the below error. Can I please get some help with this? Thank you. Also, I am using Windows. And I have both AutoDock.exe and…

TL;DR: I try to learn how to improve the prediction of spectra (mainly IR, UV/vis and NMR) and calculate Boltzmann weights from iMTD-GC calculations using CREST and I don’t really understand the software’s output. First question is for my comprehension, second one CREST specific, 3-5 general questions. CREST has been…

Just finished PhD (computational chemistry with strong ML/AI focus). I’d like to stay in research, specifically more on the software/tech side of things, but still slightly involved in physics/chemistry. I have two offers: National lab postdoc paying $85k. They tell me this position has a “high chance of transitioning to…

I ran an HF calculation in Gaussian with the option formchk, and I’d like to take a look at the output orbitals. Usually I would use Gaussview, but our HPC system’s interactive desktop is down right now. The Gaussian documentation states:” formchk converts the data in a Gaussian checkpoint file…

I have the code with me. But I’m not able to interpret the results. I’m not even sure I understand the code in its full entirety. I’ll attach the code as well for your understanding. Please help me out with this. Please. Q1. Write A molecular dynamics code interacting with…

Thing I want to do – Simulated Annealing of a Polymer Methodology I am following – Create a Polymer chain of desired length. Use PACKMOL to pack desired number of chains in a conveniently huge box. Using LAMMPS follow the general equilibration protocol, NVE, NVT, NPT dynamics. Shrink the box…

I have just started working in the field of molecular dynamics and using gromacs for my studies. The problem that I am facing is topology generation for non-standard molecules. I looked into the gromacs manual on how to add residue to a forcefield but that is quite confusing. I started…