What is AmberTools?

Amber is a suite of biomolecular simulation programs. Second, it is a package of molecular simulation programs which includes source code and demos. Amber is distributed in two parts: AmberTools21 and Amber20. You can use AmberTools21 without Amber20, but not vice versa.

What is Pmemd?

PMEMD (Particle Mesh Ewald Molecular Dynamics) is the primary engine for running molecular dynamics simulations with AMBER, and it provides the ability to use NVIDIA GPUs to greatly decrease the time it takes to run explicit and implicit solvent simulations in comparison to sander.

Are AmberTools free?

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses.

Where is AmberTools installed?

There is a couple of differences to the installation from source described below: AmberTools end up in a folder /opt/amber17 not /opt/amber16.

How do you cite the Amber20?

When citing Amber20 or AmberTools21 please use the following: D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, S.R.

What is Pmemd Cuda?

The single GPU version of PMEMD is called pmemd. cuda while the multi-GPU version is called pmemd. cuda. Note the CPU compiler has little effect on the performance of the GPU code and so, while the Intel compilers are supported for building the GPU code, the recommended approach is to use the GNU compilers.

What is OPLS force field?

The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.

What is MMFF94?

The MMFF94 force field (and the related MMFF94s) were developed by Merck and are sometimes called the Merck Molecular Force Field, although MMFF94 is no longer considered an acronym. The method provides good accuracy across a range of organic and drug-like molecules.

What is amber in computational chemistry?

Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman’s group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields.