It is used by NAMD to run the simulation, basically a list of all the bonds, angles, dihedrals, improper and VdW terms. (there are different types of these depending on the classes of molecules you have in your model, such as lipids or DNA). Par_all27_prot_na.par - a parameter file. This has to be the same order as the psf file. The actual starting coordinates of the models. A list of the atoms, masses, charges and connections between atoms. To run a molecular dynamics simulation on a cluster, the minimum files we need are: In the previous introductory tutorial we simply launched a short job on the cluster that already had all the required input files to simulate a ubiquitin protein molecule in solution. 2 - NAMD overview ¶ a) Recap: what we’ve done so far ¶ Tip: in conjunction with this tutorial there are some excellent NAMD tutorials available that are worth working through. It is assumed that the user has a basic command of visualization programs such as VMD and has had at least some experience launching and retrieving example tutorial jobs to the cluster, as shown in our introductory molecular dynamics tutorial. The aim of this tutorial is to give more advanced lessons in setting up and preparing molecular dynamics jobs for submission to the HPC cluster. Tutorials created by Mike Kuiper, edited by Thomas Coudrat. Note: this tutorial describes the use of Snowy, but all these steps can be carried out on Barcoo by substituting every instance of snowy for barcoo. Login on, select ‘Software agreement’, ‘Add software’, ‘NAMD’. Users are required to agree to these requirements to use NAMD on the Melbourne Bioinformatics HPC clusters. Important: NAMD has specific licencing requirements. Please bring along your laptops with the following installed before arriving: If you are not familiar with using the command line, please also attend the Introduction to Unix workshop. It is recommended that participants attend Introduction to High Performance Computing prior to this workshop. This workshop is intended for scientists interested in learning the basics of running molecular dynamics on a HPC cluster. Download the output and visualise the preliminary results.Submit a basic molecular dynamics job on the cluster.Log onto a high performance computer cluster.Finally we will download the results back to our local computer to visualize with VMD.Īt the end of the course, you will be able to: We then upload this directory to the cluster where we submit the job. We initially download a copy of the directory to our local computer where we then build up the input files using VMD. MD tutorial - Building input files (this tutorial): In this tutorial we will be introducing a more sophisticated directory structure using scripts to direct the output and run the job. Once the job is finished, we will download the data to your local computer and visualize the trajectory with VMD. Here we will simply copy across a bare minimum directory containing input files ready to go for a short NAMD simulation. MD tutorial - Introduction to cluster computing: If you have never launched a job on a cluster before, this tutorial is for you. Each tutorial is designed to be stand alone, start where you feel most comfortable and skip the exercises that are too simple. As students have a vast range of skill levels and requirements, the tutorials are divided into two parts described below. In the following tutorials we will be logging on a high performance computer (HPC) to submit NAMD molecular dynamics (MD) jobs and visualising the results with the molecular visualization program VMD. Molecular Dynamics Tutorial - Building input files, visualising the trajectory ¶ Overview ¶ Molecular Dynamics - Building input files, visualising the trajectoryĬ) The Namd_intermediate_template directory structureī) Molecular dynamics trajectory smoothing Molecular Dynamics - Introduction to cluster computing Identifying proteins from mass spectrometry data RNAseq differential expression tool comparision (Galaxy) Introduction to Metabarcoding using Qiime2 Hybrid genome assembly - Nanopore and Illumina Introduction to de novo genome assembly for Illumina readsĭe novo assembly of Illumina reads using Velvet (Galaxy)ĭe novo assembly of Illumina reads using Spades (Galaxy) Introduction to de novo assembly with Velvet
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