In order to build input files for NAMD, we will need a pdb file giving the initial coordinates. We will now go through the process of building a NAMD input files from scratch. In our introductory tutorial all we had to do was launch the job. Tells the cluster how to run the NAMD job and how many cores to use. Sbatch_batchfile - a script file to launch the job on the cluster depending on the scheduler used (i.e. 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.
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