Using Blueridge and Installing GROMACS

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<p>This page will walk you through the basic steps of accessing Blueridge from any computer and installing GROMACS. Blueridge is one of Virginia Tech's supercomputers that we will run our molecular modeling on. If you are confused on a step or what commands to use ASK SOMEBODY. You can bring down the system or delete your own data. These guides are relatively comprehensive, but are not exhaustive. Google will be your best friend when finding your way through a new system such as this. If you are on a lab computer, or on a computer running Linux you do not have to install a SSH (secure shell) or SFTP (SSH File Transfer Protocol) client, we have already done so. In order to connect to Blueridge from a personal computer you must install a VPN (virtual private network) and a SSH/SFTP client. A VPN is very useful to have as it will not only let you connect to Blueridge, but it will let you access all of Virginia Tech's academic journals the university has subscribed to and download software from the software bundle when off campus. You will need a VPN anytime you want to connect to a Virginia Tech service while off Virginia Tech's wifi or ethernet. SSH allows you to remotely access Blueridge and run jobs or commands. SFTP allows you to transfer files between your local computer and the super computer.</p> <h2>Installing a VPN</h2> <p><a href="https://vt4help.service-now.com/kb_view_customer.do?sysparm_article=KB0010740" rel="nofollow">This guide</a>, put out by Virginia Tech, will walk you through all steps on installing a VPN for a Mac or Windows computer. </p> <h2>Installing a SSH/SFTP Client</h2> <p>If you are on a Mac you are in luck, the Mac terminal has the native capability of SSH and SFTP, so you don't need to install anything extra. For Windows users there are endless clients out that will do SSH and SFTP. <a href="http://www.putty.org/" rel="nofollow">PuTTY</a> is a popular SSH client, and <a href="https://winscp.net/eng/docs/free_sftp_client_for_windows" rel="nofollow">WinSCP</a> is a popular SFTP client. There are multiple out there, so use whatever works best for you. Remember, these will not be able to access BlueRidge without your VPN up and running.</p> <h2>Using Blueridge and Installing GROMACS</h2> <p>This guide will walk you through the basics of moving through the supercomputer and installing GROMACS onto it. <strong>Before you install GROMACS check with Dr. Brown what version you will be using.</strong> If you use a different version than the rest of your group partners the results will not be comparable. Follow along with <a href="https://drive.google.com/open?id=1nKT40UShjJ1-u8yttMU-YMhamHhlMGSgoSj5qfiMbEA" rel="nofollow">this guide</a> and ask any questions that a quick Google search will not answer. It is much easier to ask now than to have to find and correct a bug in the future. It should be noted that the majority of steps will take place within your terminal or command prompt, so when told to type something, type it in a terminal. Copying and pasting longer commands will help ensure that no typos are made. </p> <h2>Automated GROMACS Installation</h2> <blockquote> <p>This guide assumes you know how to put files on your computing cluster. If this is not the case, please read the following tutorial. The character “$$” indicates a command line for you to type. Do not type the “$”. Systemname is either cascades, blueridge, newriver… or a newer system! <a href="https://docs.google.com/document/d/1nKT40UShjJ1-u8yttMU-YMhamHhlMGSgoSj5qfiMbEA/edit" rel="nofollow">Learn More</a></p> </blockquote>
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