Tag: comp_chem

Bound State of a Protein through kmeans (or GMVAE) Clustering : comp_chem

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…

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Ready to use Machine learning models to predict a property. : comp_chem

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…

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Question about MD lammps : comp_chem

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…

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Bio/pharma vs. materials – can anyone speak of specializing in either of these? : comp_chem

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…

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Comp chem career path advice? : comp_chem

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…

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Structure relaxation using SIESTA : comp_chem

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…

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Visualisation for MD simulations data : comp_chem

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…

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Error with running AutoGrid- AutoDock4 : comp_chem

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…

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Improving IR, UV/vis and NMR calculations by CRE sampling : comp_chem

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…

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Postdoc or industry scientist job? : comp_chem

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…

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Gaussian Fchk- What visualization programs? : comp_chem

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…

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Can anyone help with understanding this Molecular Dynamics Simulations (in FORTRAN) problem? : comp_chem

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…

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Help with LAMMPS : comp_chem

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…

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Topology generation for non-standard molecules in GROMACS : comp_chem

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…

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