A Python tool to set up relative free energy calculations in GROMACS

نویسندگان
چکیده

برای دانلود باید عضویت طلایی داشته باشید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

A Python tool to set up relative free energy calculations in GROMACS

Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of findi...

متن کامل

g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations

Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GR...

متن کامل

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

Our interest is relative binding free energy (RBFE) calculations based on molecular simulations. These are promising tools for lead optimization in drug discovery, computing changes in binding free energy due to modifications of a lead compound. However, in the "alchemical" framework for RBFE calculations, some types of mutations have the potential to introduce error into the computed binding f...

متن کامل

Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years seve...

متن کامل

Mathematica as a Versatile Tool to Set-up and Analyze Neutronic Calculations for Research Reactors

Modern technical computing environments, such as Mathematica or Matlab, provide powerful tools and techniques for research reactor analysis combined with advanced graphical user interfaces. In addition, reactor calculations can now be efficiently supported by neutronics codes based on the Monte Carlo method due to the dramatic increase of computer performance in recent years. In particular for ...

متن کامل

ذخیره 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 Computer-Aided Molecular Design

سال: 2015

ISSN: 0920-654X,1573-4951

DOI: 10.1007/s10822-015-9873-0