Difference between revisions of "AMBER"

Latest revision as of 04:30, 18 October 2024

Description

Amber is a suite of biomolecular simulation programs. The term "Amber" refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules; these force fields are in the public domain, and are used in a variety of simulation programs. Second, it is a package of molecular simulation programs which includes source code and demos.

Amber is distributed in two parts: AmberTools24 and Amber24. See the Download Amber link for information on how to download the code.

Amber is developed in an active collaboration of David Case at Rutgers University, Tom Cheatham at the University of Utah, Ray Luo at UC Irvine, Ken Merz at Michigan State University, Maria Nagan at Stony Brook, Dan Roe at NIH, Adrian Roitberg at the University of Florida, Carlos Simmerling at Stony Brook, Junmei Wang at the University of Pittsburgh, Darrin York at Rutgers University, and many others. Amber was originally developed under the leadership of Peter Kollman.

A good general overview of the Amber codes can be found in:

R. Salomon-Ferrer, D.A. Case, R.C. Walker. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 3, 198-210 (2013).

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).

D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruzeiro, N. Forouzesh, T.J. Giese, A.W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M.C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M.R. Machado, H.M. Nguyen, K.A. O’Hearn, A.V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T.E. Cheatham III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan*, and K.M. Merz Jr.* AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023).

See https://ambermd.org/AmberModels.php for information about force fields.

Required Modules

For more details on specific modules required for different versions of AMBER, run module spider amber. We currently support amber/24 (with cuda/12.4.1 openmpi/4.1.6 and gcc/12.2.0). Note that the Amber/24 (and Amber in general) is provided to HiPerGator users by the courtesy of Prof. Adrian Roitberg. Amber users are encouraged to register with Amber by downloading FREE version from https://ambermd.org/GetAmber.php. Amber developers appreciate the courtesy.

System Variables

HPC_AMBER_DIR - installation directory
HPC_AMBER_BIN - executable program directory
HPC_AMBER_LIB - library directory
HPC_AMBER_INC - include file directory

Citation

See https://ambermd.org/CiteAmber.php for how to cite Amber.

@@ Line 1: / Line 1: @@
-[[Category:Software]]
+[[Category:Software]][[Category:Chemistry]][[Category:Molecular Dynamics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|Amber}}
@@ Line 6: / Line 6: @@
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
 |{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
-|{{#vardefine:pbs|1}}            <!--PBS SCRIPTS-->
+|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
 |{{#vardefine:testing|}}       <!--PROFILING-->
@@ Line 18: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-'''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.
+Amber is a suite of biomolecular simulation programs. The term "Amber" refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules; these force fields are in the public domain, and are used in a variety of simulation programs. Second, it is a package of molecular simulation programs which includes source code and demos.
-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).
+Amber is distributed in two parts: AmberTools24 and Amber24. See the Download Amber link for information on how to download the code.
-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).
+Amber is developed in an active collaboration of David Case at Rutgers University, Tom Cheatham at the University of Utah, Ray Luo at UC Irvine, Ken Merz at Michigan State University, Maria Nagan at Stony Brook, Dan Roe at NIH, Adrian Roitberg at the University of Florida, Carlos Simmerling at Stony Brook, Junmei Wang at the University of Pittsburgh, Darrin York at Rutgers University, and many others. Amber was originally developed under the leadership of Peter Kollman.
-== Version ==
+A good general overview of the Amber codes can be found in:
-The default version is ''Amber 12'' with subversion: Amber 12.21 and AmberTools 13.23
-<!--Modules-->
+R. Salomon-Ferrer, D.A. Case, R.C. Walker. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 3, 198-210 (2013).
-==Required Modules==
-===Serial===
-* intel/2013
-* amber
-Example:
+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).
- module load intel/2013 amber
-===Parallel (MPI)===
+D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruzeiro, N. Forouzesh, T.J. Giese, A.W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M.C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M.R. Machado, H.M. Nguyen, K.A. O’Hearn, A.V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T.E. Cheatham III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan*, and K.M. Merz Jr.* AmberTools. J. Chem. Inf. Model. 63, 6183-6191 (2023).
-* intel/2013
-* openmpi
-* amber
-Example:
- module load intel/2013 openmpi amber
-===GPU (Serial)===
-* intel/2013
-* cuda
-* amber/12-cuda
-Example:
- module load intel/2013 cuda amber/12-cuda
-===GPU (Parallel/MPI)===
-* intel/2013
-* openmpi
-* cuda
-* amber/12-cuda
-Example:
- module load intel/2013 openmpi cuda amber/12-cuda
+See https://ambermd.org/AmberModels.php for information about force fields.
+==Required Modules==
+For more details on specific modules required for different versions of AMBER, run <code>module spider amber</code>. We currently
+support amber/24 (with cuda/12.4.1 openmpi/4.1.6 and gcc/12.2.0). Note that the Amber/24 (and Amber in general) is provided to HiPerGator users by the courtesy of Prof. Adrian Roitberg. Amber users are encouraged to register with Amber by downloading
+FREE version from https://ambermd.org/GetAmber.php. Amber developers appreciate the courtesy.
 ==System Variables==
-* AMBERHOME
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable program directory
-* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable program directory
+* HPC_{{uc:{{#var:app}}}}_LIB - library directory
-* HPC_{{#uppercase:{{#var:app}}}}_LIB - library directory
+* HPC_{{uc:{{#var:app}}}}_INC - include file directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 75: / Line 50: @@
 WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 |}}
-<!--PBS scripts-->
+<!--Job scripts-->
-{{#if: {{#var: pbs}}|==PBS Script Examples==
+{{#if: {{#var: pbs}}|==Job Script Examples==
-See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
+See the [[{{PAGENAME}}_Job_Sample_Scripts]] page for {{#var: app}} Job script examples.
 |}}
 <!--Policy-->
@@ Line 91: / Line 66: @@
 *'''Q:''' **'''A:'''|}}
 <!--Citation-->
 {{#if: {{#var: citation}}|==Citation==
-===Serial Version===
+See https://ambermd.org/CiteAmber.php for how to cite Amber.
-If you publish research that uses {{#var:app}} you have to cite it as follows: <br/>
-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. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, 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, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.
-===GPU Version===
-If you make use of any of this GPU support in your work please use the following citations: <br/>
-Andreas W. Goetz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le Grand;  & Ross C. Walker* "Routine microsecond molecular dynamics simulations with AMBER - Part I: Generalized Born", J. Chem. Theory Comput., 2012, 8 (5), pp 1542-1555 , DOI: 10.1021/ct200909j
-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. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, 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, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.
 |}}