MkVsites : A tool for creating GROMACS virtual sites parameters to increase performance in all‐atom molecular dynamics simulations
نویسندگان
چکیده
منابع مشابه
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
1Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3 Theoretical and Computational Biophysics Dept., Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 4Center for Biomembrane Research, Dept. Biochemistry & Biophysics, Stockholm University, SE...
متن کاملPerformance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The ...
متن کاملMolecular dynamics simulations as a tool for improving protein stability.
Haloalkane dehalogenase (DhlA) was used as a model protein to explore the possibility to use molecular dynamics (MD) simulations as a tool to identify flexible regions in proteins that can serve as a target for stability enhancement by introduction of a disulfide bond. DhlA consists of two domains: an alpha/beta-hydrolase fold main domain and a cap domain composed of five alpha-helices. MD simu...
متن کاملPutative Binding Sites of Dopamine and Arachidonoyl Dopamine to Beta-lactoglobulin: A Molecular Docking and Molecular Dynamics Study
Because of participation in many aspects of human life, and due to oxidation-sensitive characteristics of dopamine (DA) and arachidonoyl dopamine (AA-DA), the necessity of biocompatible carrier to keep them against oxidation is of importance. In this work, we explored the putative binding sites of DA and AA-DA to -lactoglobulin (BLG) as potent carrier. Docking results identified the binding si...
متن کاملDeducing hydration sites of a protein from molecular dynamics simulations.
Invariant water molecules that are of structural or functional importance to proteins are detected from their presence in the same location in different crystal structures of the same protein or closely related proteins. In this study we have investigated the location of invariant water molecules from MD simulations of ribonuclease A, HIV1-protease and Hen egg white lysozyme. Snapshots of MD tr...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2020
ISSN: 0192-8651,1096-987X
DOI: 10.1002/jcc.26198