I have been working MD simulation in windows using NAMD and Charm GUI but it take lots of time to run even for 10ns. I have a workstation having 64gb RAM, 8 core and 16 process with graphic card. we can use multiple core using MPI but do not know how to intsall and run the program. Can anyone help me the process of installation and working to run MD simulation using NAMD and CHARM GUI
Follow these steps:
1. Launch the CHARMM-GUI interface: Start the CHARMM-GUI interface on your Windows system.
2. Set up your MD system: Use the CHARMM-GUI interface to set up your MD system by providing the necessary input files such as protein structure, parameter/topology files, and simulation parameters.
3. Configure the simulation settings: In the CHARMM-GUI interface, you should find options to configure the simulation settings. Look for the option that allows you to specify the number of cores or processors to be used for the simulation.
4. Specify the number of cores: Increase the number of cores or processors to the desired value, depending on the resources available on your system. Usually, this option is labeled as "Number of Cores" or "Number of Processors" and can be found in the simulation settings or system configuration section.
5. Submit the simulation: Once you have set up the simulation settings and specified the number of cores, submit the simulation through the CHARMM-GUI interface. The interface will generate the necessary NAMD input files and launch the simulation using the specified number of cores.
Good luck
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