Essays about: "gaff"

Found 2 essays containing the word gaff.

  1. 1. Atomistic Modeling of Amorphous Energetic Materials

    University essay from Uppsala universitet/Molekyl- och kondenserade materiens fysik

    Author : Pontus Melin; [2018]
    Keywords : amorphous; energetic; materials; molecular dynamics; MD; CL-20; HMX; PVAc; gaff;

    Abstract : A majority of research within the field of energetic materials have been centered around the stable crystalline phase, whilst there has been less about the amorphous phase and the implications of these types of material. In this study, Molecular Dynamics simulations with the General Amber Force Field (GAFF) is used to predict fundamental properties of the nitramine explosives HMX and CL-20 in the amorphous phase. READ MORE

  3. 2. Using Molecular Dynamics and Enhanced Sampling to Predict Binding Poses Beyond The Rigid-Docking Approximation

    University essay from Lunds universitet/Biofysikalisk kemi

    Author : Emil Åberg; [2017]
    Keywords : GAFF; FXR; farnesoid X receptor; MD; computational; enhanced sampling; binding; receptor; ligand; Simulations; Reconnaissance; Metadynamics; Docking; Molecular Dynamics; Protein; AMBER; force fields; structure prediction; crystallography; collective variables; potential; bias potential; biophysical chemistry; biofysikalisk kemi; Chemistry; Technology and Engineering; Biology and Life Sciences;

    Abstract : A computational method is described and tested for prediction of ligand-binding poses between the human farnesoid X receptor and a set of 36 potential agonists, provided by the D3R Grand Challenge 2016. Using tools such as Molecular Docking, Molecular Dynamics, Reconnaissance metadynamics and cluster analysis, the method is an attempt to predict the binding pose without being biased by experimental data. READ MORE