My program (working name is JuliaMD), can now detect isolated aromatic rings, and has more complete atom typing, which allows better simulations with the gaff2 forcefield. I haven't yet implemented specific aromatic atom types, but after the ring detection tool it will be easy to do.
Here is the link to the video, just out of the oven!
Here is a small update (2 min video) on the features I have added to my Molecular Dynamics with Julia project.
Combination of relaxed surface scans with molecular dynamics can be used to sample conformations while scanning the distance between two atoms in a reaction. This you get error bars for your energies which give a more robust estimation of activation energies.
this is my latest video on the molecular dynamics with Julia series. I sort of fixed part of the polymer builder tool, by improving the monomer conformation (NIPAM forms thermoresponsive polymers and is somewhat bulky). I also show my (so far failed) attempts at automatic optimization of residue rotation to minimize steric hindrance between residues.
Last night I released a video simply discussing what I have been doing lately with my program for molecular dynamics with Julia. It was different in that it was just me talking. I have thought for long on making more videos just discussing aspects of computational chemistry, research, academia, etc, but I always feel that I'm not expert enough in any of the particulars I want to talk about. However, I do have a lot of things I would like to say. So I was just wondering if anyone has some general questions that you would like me to address in future videos. It can be about methodology or more general philosophical types of questions. If I feel confident, after doing some reading I can perhaps answer them in short videos.
P.s. I won't post a link, and if you don't know who I am you can search in some of my other posts in the sub
This is an update from my previous post on a simple molecular visualizer in Julia. Now it has colors, and I can also visualize simultaneously the energies, highlighting the energy for the particular structure I'm watching. I will continue to add functionality.
This is a very short preview of a new tool I'm making as part of my MD of Polymers with Julia series. In the following days I will make it so that different elements (C, H, O, N, etc) have different colors and sizes.
Following my project to do molecular dynamics of polymers with Julia and Orca, I'm showing a set of tools to read Orca relaxed surface scan trajectories, energies of optimized steps in a scan, and Loewdin charges of each step from the scan, parsing the output file. this will make it easier to least squares fit force field terms to the energy profiles for bond, angle or torsion scans.
Link below to the latest video in the series:
Following my project to do molecular dynamics of polymers with Julia and Orca, I'm showing a set of tools to read Orca relaxed surface scan trajectories, energies of optimized steps in a scan, and Loewdin charges of each step from the scan, parsing the output file. this will make it easier to least squares fit force field terms to the energy profiles for bond, angle or torsion scans.
I do a lot of computational chemistry on organic and organometallic compounds. But I seldom do any kind of predictive work, mainly because no one has asked me to and my type of work does not require it. But I was thinking, what would be useful for a synthetic organic chemist in advance of trying new synthesis routes?
As an example, could be:
The best solvent for a particular reaction and reactants?
Computational screening of Lewis acid or base catalysts?
Solubility of reactants or products in a given solvent (mixture)?
Finding the plausibility of side reactions involving the components of the reaction system?
Estimating reaction barriers/constants?
What else?
I would leave out complicated organometallic catalysts for now.
Hi, this is the next part in the MD of Polymers with Julia series. Here I set up an N-isopropylacrylamide (NIPAM) monomer to use with a polymer chain builder script that I made in Julia. I go over some of the things to take into account and how to solve some of the issues. It's a longish video.
This is a short teaser for my upcoming video on the topic in the title, showing the linear polymer chain generation script, using polyacrylamide as an example. I wanted to embed the video directly here but I don't find the option, so here is the link
Here is a small update showing the automated atom type assignment, as well as plans for the following weeks: GAFF and Orca
I'm making an MD tool using molly.jl, on top of which I'm adding functionality to automatically generate topologies and force field parameters starting from XYZ files. If someone is interested please check it out! Thank you!
I wanted to share a video on a project I've been working on, aiming at simple molecular dynamics of synthetic polymers using Julia and Molly.jl. The program (work in progress) is meant to automatically generate a topology given an XYZ file or string, and generate crude FF parameters based on automatically detected atom types. This information is collected in Molly formatted variables, allowing (in the future) a simulation with minimal user input. The purpose at this point is not to make accurate MD, but to generate better starting structures for subsequent MD simulations.
Please see the link below. All suggestions and comments are wellcome (especially in YT) !
Thanks!
I made a bodipy, and it stuck to the silica! Eluting with a high polarity mixture now
edit: I have 4-methylcarboxyphenyl as the meal aryl group. is it possible that BF3-Et2O if not dry causes hydrolysis of the water group, giving me a very polar BODIPY?
Dipyrromethane we made yesterday and filtered today. The vial is 10 ml, and we should have between 2 and 2.5 grams of compound (plus a lot of moisture at this stage)