Move inside this new directory and install as shown below. It will create a new directory, namely, vmd-1.9.3.
Let’s say we have downloaded this file in the Downloads directory. Go to the directory where you have downloaded the tar file and extract. Here, we are downloading VMD 1.9.3, not the latest alpha version as it is a test version, therefore, you might face some issues. After successful registration, it will automatically start downloading.
#Install vmd download
To download VMD, you will have to register using your university email address. Go to this page and select an appropriate VMD version compatible with your system. Open a terminal by pressing Ctrl+Alt+T and paste the following commands.
#Install vmd update
Update and upgrade your system before installing VMD. Journal of molecular graphics, 14(1), 33-38.In this article, we are going to install VMD on Ubuntu. Humphrey, W., Dalke, A., & Schulten, K.In SC’02: Proceedings of the 2002 ACM/IEEE conference on Supercomputing (pp. NAMD: Biomolecular simulation on thousands of processors. QwikMD-Gateway for Easy Simulation with VMD and NAMD. C., Rudack, T., Schulten, K., & Tajkhorshid, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.
J., Murtola, T., Schulz, R., Páll, S., Smith, J. The live simulation will be continued to run in the background until you abort it. It might show an error (” Error connecting to localhost on port 3000“) until a connection is established between NAMD and VMD. Here, the temperature was set to 27 C (300 K) and the simulation time was set to 1ns.Ĭlick 'Start MD Simulation'-> Select the number of CPU cores to be used to perform the simulation. All files created during the set up will be stored in the setup folder and those files that will be required for running MD simulation will be stored in run folder.Ĭheck the 'Equilibration' and 'MD' checkboxes and enter particular 'Temperature' and 'Simulation time'. You will have to select a folder to save the input file named ‘.qwikmd‘.Īfter that, you will notice two folders will be created in the working directory: setup and run. Now, move to the section ‘Simulation Set up’.Ĭheck the 'Live View' checkbox for Live simulation and click 'Prepare'.ĭuring this step, autopsf function is called to generate files required for MD simulation including NAMD configuration files. Here, it is ‘implicit’ and default salt concentration (0.15 mol/L).Ħ. Select the ‘Solvent’ and ‘Salt concentration’. Remove oxygen atoms from water molecules.Ĭlick on 'Chain/Type Selection' and deselect the water molecules 'A and water'.Īfter that, you can see the oxygen atoms (red) in the VMD display will disappear.ĥ. We are performing a simple MD and we will be using implicit solvent method.Ĥ. For more information regarding this, click here. It allows users to either simulate in an explicit solvent by simulating all atoms of the solvent or in an implicit solvent by adding a dielectric constant to the electrostatic calculation. Now, load your protein structure either by typing or by browsing, then Click 'Load'. 1 A screenshot of QwikMD window launched from VMDģ.