My internet was out at home for the past week, so I haven't been able to post.\
I've finally begun my project. Over the course of the past week, I took the initial structure, solvated it, added ions, minimized it, and soon (if the queue ever clears) will begin equilibration. I started with a file called a .pdb file which contained information about the structure of the minimal length HHR I'm studying. I then modified this in a program called Amber by adding ions to balance excess negativity, solvating the system in a box of waters, and then bringing the solution up to .14M concentration NaCl, as well as updating it with new water and ion models. I then minimized the system using the program sander. When I and the researchers helping me took a look at the out put files, we discovered that all the ions had decided to clump up into a ball in one corner of our box (which makes sense to the model, but physically is not observed), so we had to use a program to manually randomize the ion positions. I then minimized the system again. That all took about a week (theses simulations take a very long time), during which time I also got another meeting with Dr. York where we discussed some of the theory behind the model I am using, and I had lunch with other high school and undergrad researchers in the physical chemistry department.
Before leaving for the day on Friday, I started running the equilibration. This essentially is a long warming up period for the system in which heat is evenly distributed across the atoms. Certain specific restraints and parameters have to be used to stop the system from heating unevenly or becoming unstable. When I came back this morning, the simulation was still running. As such, I've been set up with an account to access the super computer at UMN, and am at this moment waiting for my equilibration to clear the queue of idle jobs and begin.
I've finally begun my project. Over the course of the past week, I took the initial structure, solvated it, added ions, minimized it, and soon (if the queue ever clears) will begin equilibration. I started with a file called a .pdb file which contained information about the structure of the minimal length HHR I'm studying. I then modified this in a program called Amber by adding ions to balance excess negativity, solvating the system in a box of waters, and then bringing the solution up to .14M concentration NaCl, as well as updating it with new water and ion models. I then minimized the system using the program sander. When I and the researchers helping me took a look at the out put files, we discovered that all the ions had decided to clump up into a ball in one corner of our box (which makes sense to the model, but physically is not observed), so we had to use a program to manually randomize the ion positions. I then minimized the system again. That all took about a week (theses simulations take a very long time), during which time I also got another meeting with Dr. York where we discussed some of the theory behind the model I am using, and I had lunch with other high school and undergrad researchers in the physical chemistry department.
Before leaving for the day on Friday, I started running the equilibration. This essentially is a long warming up period for the system in which heat is evenly distributed across the atoms. Certain specific restraints and parameters have to be used to stop the system from heating unevenly or becoming unstable. When I came back this morning, the simulation was still running. As such, I've been set up with an account to access the super computer at UMN, and am at this moment waiting for my equilibration to clear the queue of idle jobs and begin.
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