Biophysical Society Thematic Meeting| Lima 2019

Revisiting the Central Dogma of Molecular Biology at the Single-Molecule Level

Poster Abstracts

44-POS Board 44 IMPLEMENTATION OF A NEW METHOD FOR GRID STEERED MOLECULAR DYNAMICS Nestor Alonso Perez Moron 1 ; Eduardo Cruz Chu 1 ; 1 Universidad Peruana Cayetano Heredia, Lima, Lima, Peru Molecular Dynamic(MD) is a computational technique that was crucial for the development of molecular biology. Nevertheless, the drawback of MD is the high computational cost, in other words, the amount of cores increment at the same time as the number of particles(a core for each 2000 atoms). Therefore, to work with big systems, it is necessary the access of unavailable clusters. For that reason, scientist have develop new methods to resolve this problems , one of them is named Grid Steered Molecular Dynamics(Grid-SMD)[1].The actual technique of Grid- SMD determinates the properties of particles in a rapid-evaluation-grid. This method only consider the electrostatic potential, and evades the Van-der-Waals(VDW) interactions. The present research accomplish an implementation of the VDW potential to the Grid-SMD method to upgrade the molecular description of the technique.To endforce the VDW-Grids, it was created a TCL script to compute VDW energy using the Lennard-Jones potential and the information from CHARMM parameters. The software required for this was VMD to visualize the simulation and NAMD to makes the simulation. The Grid-SMD simulation was develop with the VDW-Grids and the Electrostatic Grid in a multiple grid simulation where the long range force and the short range force was cover.For the testing part, we use the MHC-II system. In the structure, we identify the MHC system and the receptor, a peptide. This simulation showed the bound between the system and the peptide. Furthermore, the time from the simulation was enormously reduced, taking over the system by the VDW-Grids, and making a simulation with the Grids and the peptide. In the other hand, further information needs to be analyze to validate the use of this implementation for interaction studies.

81