Difference between revisions of "AMBER"

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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{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).
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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).  
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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 ==
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A good general overview of the Amber codes can be found in:
Due to its license policy, users who wish to use it will need to obtain the permission from Dr. Adrian Roiberg and submit a help request at: http://support.rc.ufl.edu. You will then be added to "amber" group (as your secondary group) for accessing Amber 16 and 18.
 
  
<!--Modules-->
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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===
 
  
'''For Amber 18:'''
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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).
  
* intel/2017
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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).  
*amber/18
 
 
 
'''For amber 16:
 
'''
 
* intel/2018.1.163
 
* amber
 
 
 
Example:
 
module load intel/2017 amber/18
 
 
 
===Parallel (MPI)===
 
 
 
'''For amber 18'''
 
 
 
* intel/2017
 
*openmpi/3.1.2
 
*amber/18
 
 
 
'''For amber/16:'''
 
 
 
* intel/2018.1.163
 
* openmpi/3.0.0
 
* amber
 
 
 
Example:
 
module load intel/2017 openmpi/3.1.2 amber/18
 
 
 
===GPU (Parallel/MPI)===
 
 
 
For amber 18:
 
 
 
* cuda/9.2.88
 
* intel/2017
 
* openmpi/3.1.2
 
* amber/18
 
 
 
Example:
 
module load cuda/9.2.88 intel/2017 openmpi/3.1.2 amber/18
 
  
 +
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==
 
==System Variables==
* AMBERHOME
 
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_BIN - executable program directory
 
* HPC_{{uc:{{#var:app}}}}_BIN - executable program directory
 
* HPC_{{uc:{{#var:app}}}}_LIB - library directory
 
* HPC_{{uc:{{#var:app}}}}_LIB - library directory
 
* HPC_{{uc:{{#var:app}}}}_INC - include file directory
 
* HPC_{{uc:{{#var:app}}}}_INC - include file directory
 
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 92: Line 54:
 
See the [[{{PAGENAME}}_Job_Sample_Scripts]] page for {{#var: app}} Job script examples.
 
See the [[{{PAGENAME}}_Job_Sample_Scripts]] page for {{#var: app}} Job script examples.
 
|}}
 
|}}
 
 
<!--Policy-->
 
<!--Policy-->
 
{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
Line 105: Line 66:
 
*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
 
<!--Citation-->
 
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
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{{#if: {{#var: citation}}|==Citation==  
===Serial Version===
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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.
 
  
 
|}}
 
|}}

Latest revision as of 04:30, 18 October 2024

Description

Amber website  

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.