Molecular Modelling - Innovation Lab 2020

You can find all the simulation files for our case study here .

Molecular dynamics-based investigation of interactions between Remdesivir analogue GS-441524 and a model human cell membrane using LAMMPS     As a case study for the Innovation Lab project we have decided to explore a topic somewhat related to the ongoing COVID-19 Pandemic. This said, in  the current race against SARS-CoV-2, interest has been drawn to Remdesivir, an antiviral approved for emergency treatment of COVID-19 in many countries. Remdesivir is a prodrug to the pharmacologically active GS-441524 and it transforms into the latter promptly after reaching the bloodstream (Scavone et al., 2020).      The purpose of this project was to predict whether GS-441524 is capable of entering a typical human cell, namely the cell of a lung wall. Since GS-441524 is a relatively hydrophilic molecule structurally resembling adenosine, we hypothesised that it might enter human cells through nucleoside transporters. To be more precise, through the human Equilibrative ...

Please download this .cpp file ; a preview isn't available.

So far the efforts into our case study resulted in a questionable simulation of an unnaturally behaving bunch of phospholipids, though it is not an issue that cannot be fixed later. To access the simulation recording, please click on the image below.

 We love hyperlinks, so here are three more leading you to yet another crucial part of our project:

 > find a new tutorial here <

We've promised to explain how to get started with LAMMPS and today's tutorial on creating data files is being uploaded this evening. Good night and good luck! > Creating Data Files <

We've asked some questions about molecular modelling in education and received some answers. They're accessible in the document below. > Survey Summary < Being quite keen on doing extra work, Marcel explains how to conduct a survey yourself, should you ever need it. > Honest Advice on Surveys <

Find out more about the software within the document linked below. > LAMMPS and its applications <

Instead of delving straight into modelling with LAMMPS, we've created a comprehensive installation guide to help you get started from scratch; find it by clicking on the image below.

As Natural Sciences students, we’re no strangers to laboratory work. Practical experiments are something we’ve all so far encountered, to a larger or smaller extent. On the other hand, despite it being something very desirable by many employers, we’ve realised that modelling what happens on a molecular level in theory is not a strong skillset of ours at all. Therefore, we believe that both gaining insight into molecular dynamics and modelling, as well as attempting to convey that knowledge to others will be a valuable experience as much as it will surely prove to be an exciting challenge. We’ll be documenting the progress of this journey of ours on this blog, so make sure to refresh the page for any updates.    Now, without further ado:    What exactly is molecular dynamics?   Computer simulations can be used to assess the behaviour of a  constantly changing , in other words a  dynamic , system. Thanks to our current understanding of classical mechanic...