![]() ![]() ![]() For example, if what we want is to run a Molecular Dynamics Simulation of 10 ns with a timestep of 2 fs at a 300 K of temperature (a standard molecular dynamics first step, to completelly equilibrate the system), we just have to write these numbers: Time Step: 2 fs, Temperature: 300 K, Total Time: 10000 ps, and Output Frequency: 500 steps. We will need to fill in the parameter fields with desired values. It can be found in the MDWeb Simulation Operations, clicking at the icon. The first thing to do then is run an operation called Simple Box Solvent Molecular Dynamics with the MD ensemble of interest (NPT, NVE or NVT). This short tutorial assumes that user have already setup a system using one of MDWeb Workflows to run a complete system preparation: GromacsWorkflowFULL, AmberWorkflowFULL, or NamdWorkflowFULL (see Setup Tutorial), or alternatively it has been prepared step by step using the appropiate MDWeb operations. Launching Molecular Dynamics Simulation. ![]() With this short tutorial, you will be able to run a Molecular Dynamics Simulation in your own machines, using files provided by MDWeb after preparing the system. MDWeb provides a friendly environment to setup new systems and run test simulations. ![]()
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