02. Solution Builder скачать в хорошем качестве

02. Solution Builder

Here is the Solution Builder tutorial. Join MolCube apps to expand your research horizons! Try it : https://apps.molcube.com/ For more information : https://apps.molcube.com/help/getting... Script : Step 1: Project Setup Hello. I will now guide you through the process of setting up a protein simulation. The initial step requires us to import our project using Solution Builder. For this project, we will be utilizing 6W81. It represents the SARS-CoV-2 main protease, M pro, in complex with an inhibitor, and is a well-studied enzyme that plays a critical role in viral replication, making it a highly significant target for antiviral drug development. Given its importance, we will use 6W81 as our project title. Now, please proceed to the 'Search for PDB Reader Project' section within Solution Builder. Here, you should locate and select 6W81, which you have already processed and prepared via the PDB Reader. This specific title indicates that the project has been prepared in advance through your work with the PDB Reader. Once selected, please click Submit to advance to the next stage. Step 2: Simulation Environment Configuration We will now proceed with configuring the simulation environment. First, let us define the boundaries of our simulation box. Please select a Cubic box with a 10 Å buffer, which is highly effective at preventing clashes with periodic images. Next, we will add salt to the system. Please select KCl and set its concentration to 0.15 M. It is imperative to leave the 'Neutralize Only' option unchecked. This ensures that the salt concentration is adjusted to physiological levels, mimicking the natural biological environment. For the temperature, please set it to 310 K. This setting is crucial for the fidelity of our simulation as it reflects body conditions. To accelerate your simulation, we recommend enabling Hydrogen Mass Repartitioning. This feature safely allows for a larger 4 fs time step. Lastly, you must select your MD engine. OpenMM is highly recommended for its exceptional GPU performance. Once all settings have been verified, please click 'Submit' to proceed to the final step We will now proceed with configuring the simulation environment. First, let us define the boundaries of our simulation box. Please select a Cubic box with a 10 Å buffer, which is highly effective at preventing clashes with periodic images. Next, we will add salt to the system. Please select KCl and set its concentration to 0.15 M. It is imperative to leave the 'Neutralize Only' option unchecked. This ensures that the salt concentration is adjusted to physiological levels, mimicking the natural biological environment. For the temperature, please set it to 310 K. This setting is crucial for the fidelity of our simulation as it reflects body conditions. To accelerate your simulation, we recommend enabling Hydrogen Mass Repartitioning. This feature safely allows for a larger 4 fs time step. Lastly, you must select your MD engine. OpenMM is highly recommended for its exceptional GPU performance. Once all settings have been verified, please click 'Submit' to proceed to the final step. Step 3: Project File Download This is the final step. Simply click the Download project button. Upon clicking, your fully configured project along with all necessary input files will be downloaded. You are now prepared to execute your molecular dynamics simulation of the 6W81 protein in a solution environment.