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NVIDIA announces MD SimCluster Project

Major performance update to GPU accelerated PMEMD released

AmberTools version 1.5 is released

Updated version of amberlite

MPI Multi-GPU Accelerated MD

NVIDIA CEO highlights AMBER GPU port

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Assisted Model Building with Energy Refinement

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 11, which is distributed by UCSF subject to a licensing agreement described below.

Amber is distributed in two parts: AmberTools (version 1.5) and Amber11. You can use AmberTools without Amber11, but not vice versa.

A good general overview of the Amber codes can be found in: D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).

An overview of the Amber protein force fields, and how they were developed, can be found in: J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001).

Please cite the use of AMBER 11 and AmberTools 1.5 as:
D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B.P. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2010), AMBER 11, University of California, San Francisco.

Amber developers, January 2012

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AmberTools 1.5 is now available!

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models. New to version 1.5 are:

AmberTools 1.5 consists of seven main codes that were previously released separately, and five new ones:

NAB build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
antechamber and MCPB Create force fields for general organic molecules and metal centers
tleap and sleap Basic preparation program for Amber simulations
sqm semiempirical and DFTB quantum chemistry program
pbsa Performs numerical solutions to Poisson-Boltzmann models
3D-RISM Solves integral equation models for solvation
ptraj and cpptraj Structure and dynamics analysis of trajectories
MMPBSA.py and amberlite Energy-based analyses of MD trajectories

Download AmberTools

Amber 11 is now available!

We are happy to announce the release (on April 25, 2010) of version 11 of the Amber software suite. (How to order.) This represents a significant update from version 10, which was released in April, 2008. The major differences include:

  • Force fields: Amber now supports most CHARMM fixed-charge force fields, including those with CMAP torsional potentials. There is also an updated version of GAFF, the general Amber force field for organic molecules.

  • A new parameterization of the generalized Born solvation model is available, optimized for peptides and proteins.

  • Expanded options exist for numerical Poisson-Boltzmann solvation calculations.

  • Solvation effects can also be estimated using a 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations.

  • There is improved integration with the Chimera visualization program, and with UCSF DOCK.

  • Simplified methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms.

  • Amber 11 includes a new implementation of the nudged elastic band model for finding low-energy pathways for conformational transitions, which can be used for only part of the system, or in explicit solvent simulations.

  • There are updated scripts for constant pH simulations and for MMPB/SA free energy calculations.

  • The "polar" version the isotropic periodic sum model has been added, along with its IPS-DFFT counterpart.

  • MD simulations using pmemd can take advantage of NVIDIA GPU cards to obtain significant speedups compared to traditional CPU codes.

General information

Code overview

The release consists of about 50 programs, that work reasonably well together. The major programs are as follows:
  • sander: Simulated annealing with NMR-derived energy restraints. This allows for NMR refinement based on NOE-derived distance restraints, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes. Sander is also the "main" program used for molecular dynamics simulations, and is also used for replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations. Sander also includes QM/MM capability.
     
  • pmemd: This is an extensively-modified version (originally by Bob Duke) of the sander program, optimized for periodic, PME simulations, and for GB simulations. It is faster than sander and scales better on parallel machines. Additionally with version 11 it includes NVIDIA GPU acceleration; hence it is generally the program of choice, unless you need options that it does not support. In the code model we are now following, sander is the vehicle to explore new features, and pmemd is a "production" code that implements sander's most-used features in a well-tested fashion that performs well in high-performance environments.
     
  • nmode: Normal mode analysis program using first and second derivative information, used to find search for local minima, perform vibrational analysis, and search for transition states.
  • LEaP: LEaP is an X-windows-based program that provides for basic model building and Amber coordinate and parameter/topology input file creation. It includes a molecular editor which allows for building residues and manipulating molecules.
     
  • antechamber: This program suite automates the process of developing force field descriptors for most organic molecules. It starts with structures (usually in PDB format), and generates files that can be read into LEaP for use in molecular modeling. The force field description that is generated is designed to be compatible with the usual Amber force fields for proteins and nucleic acids.
     
  • ptraj: This is used to analyze MD trajectories, computing a variety of things, like RMS deviation from a reference structure, hydrogen bonding analysis, time-correlation functions, diffusional behavior, and so on.
     
  • mm_pbsa: This is a script to automate post-processing of MD trajectories, to analyze energetics using continuum solvent ideas. It can be used to break energies energies into "pieces" arising from different residues, and to estimate free energy differences between conformational basins.

 

Benchmarks

Downloads

Amber-related links

The force field

How to obtain the Amber11 program package

General correspondence

The AMBER Mail Reflector

 The Mail Reflector exists to provide a forum for discussions on the use of the Amber software and for release of bugfixes. Before posting please read the manual, consult the FAQ, and search the previous items discussed on the Amber Reflector using the Google search box provided on the archive site.
Mail reflectors distribute mail sent to the reflector address to all subscribers.

Only subscribers to the reflector can post. To join/unjoin the reflector, please see: http://lists.ambermd.org/mailman/listinfo/amber
To post or mail to the list (subscribers only), e-mail (in plain text) to:

Please use this list for discussion of Amber-specific issues only; in particular, announcements of general interest to the online chemistry community should be sent to the community's main reflector, chemistry@ccl.net. Amber users are encouraged to join this list as well, since it has a lot of useful information and since many other programs also use the Amber force fields.

Amber developers

 Amber is developed in an active collaboration of David Case at Rutgers University, Tom Cheatham at the University of Utah, Ken Merz and Adrian Roitberg at Florida, Carlos Simmerling at SUNY-Stony Brook, Ray Luo at UC Irvine, Junmei Wang at UT Southwestern, Ross Walker at UC San Diego, and many others. Amber was originally developed under the leadership of Peter Kollman.

The photo at the left shows the Amber crew at its October, 2004 meeting in Stony Brook.

Below that is a group photo a joint CHARMM/Amber developers' meeting held in San Diego in July, 2003.

At the bottom left is an older photo of Amber developers, from a meeting in San Francisco in November, 2001:
front row:Jim Caldwell, Kennie Merz, Carlos Simmerling, Ray Luo
back row:Dave Case, Piotr Cieplak, Mike Crowley, Tom Cheatham, Tom Darden, Junmei Wang.

And, below, a older photo of Peter and Tom Cheatham, followed by a photo of the participants at the February, 2007 Amber Developers' Meetings on St. Simon Island, Georgia; more recent photos then follow.

St. Simon Island, 2009

Stony Brook, 2010

Athens, Georgia, 2011

Rutgers, 2012

The Amber 11 authors are: D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B.P. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko and P.A. Kollman. Many people not listed in the author list helped add features to various codes; these contributions are outlined here.

Research support from DARPA, the NIH, and the NSF for Peter Kollman is gratefully acknowledged, as is support from the NIH, ONR and DOE for David Case. Use of the facilities of the UCSF Computer Graphics Laboratory (Thomas Ferrin, PI) is appreciated. Scott Brozell acknowledges the use of computational facilities at the Ohio Supercomputer Center. NAB was developed with support from the NIH Research Resource on Multiscale Modeling Tools for Structural Biology.

Amber developers at work Amber developers at play

A trip down memory lane

Here are some timings for a standard Amber benchmark, but over about a decade of code changes. The benchmark is "jac", which is dihydrofolate reductase (159 residue protein) in TIP3P water (23,558 total atoms). PME is used for electrostatics, and van der Waals interactions are truncated at 9 Ang. The table shows speeds for running 1000 steps (with a time step of 1 fs) on a single cpu (Intel Xeon x86_64, 3.4 GHz). All codes were compiled with the Intel ifort compiler, version 9.0.

Notes: Amber 4.1 and 5 required one to force frequent list updates in order to conserve energy, and such timings are shown below; using default parameters for those codes give timings about equal to Amber 7. Versions 6-10 give identical results for this test, up to roundoff errors. Timings for versions 4.1 to 7 are for sander, those for versions 8 to 10 are for pmemd.

CodeRelease datespeed, ps/day
Amber 4.1June, 1995103
Amber 5November, 1997104
Amber 6December, 1999121
Amber 7March, 2002135
Amber 8March, 2004179
Amber 9March, 2006249
Amber 10April, 2008314

So, the current code is more than twice as fast as it was 6 years ago. These numbers don't factor in changes in hardware speed. As one point of reference, my (DAC) desktop computer in 2000 was an SGI 250MHz R10000 machine. That machine, using Amber 6, ran this benchmark at a speed of 12 ps/day(!). On the other end, in 2010, a single Tesla C2050 GPU card runs this benchmark at over 11 ns/day (more information is here).

The parallel scaling of Amber has also improved a lot recently, but that is another story. As a simple example, this benchmark runs at 4.9 ns/day on a single (dual-quad) node "Nehalem" workstation (X5570, 2.93 GHz).

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