Difference between revisions of "AMBER"

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[[Category:Software]]
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[[Category:Software]][[Category:Chemistry]][[Category:Molecular Dynamics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|Amber}}
 
|{{#vardefine:app|Amber}}
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'''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''' 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 distributed in two parts: AmberTools12 and Amber12. You can use AmberTools12 without Amber12, but not vice versa. See below for information on how to obtain Amber12.
 
  
 
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).
 
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).  
 
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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== Version ==
 +
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-->
 
<!--Modules-->
 
==Required Modules==
 
==Required Modules==
 
===Serial===
 
===Serial===
 +
 +
'''For Amber 18:'''
 +
 +
* intel/2017
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*amber/18
 +
 +
'''For amber 16:
 +
'''
 +
* intel/2018.1.163
 
* amber
 
* amber
 +
 +
Example:
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module load iintel/2017 amber/18
 +
 
===Parallel (MPI)===
 
===Parallel (MPI)===
* intel
+
 
* openmpi
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'''For amber 18'''
* amber
+
 
===GPU (Serial)===
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* intel/2017
* intel
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*openmpi/3.1.2
* cuda
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*amber/18
 +
 
 +
'''For amber/16:'''
 +
 
 +
* intel/2018.1.163
 +
* openmpi/3.0.0
 
* amber
 
* amber
 +
 +
Example:
 +
module load intel/2017 openmpi/3.1.2 amber/18
 +
 
===GPU (Parallel/MPI)===
 
===GPU (Parallel/MPI)===
* intel
+
 
* openmpi
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For amber 18:
* cuda
+
 
* amber
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* 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
  
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* AMBERHOME
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 +
* HPC_{{uc:{{#var:app}}}}_BIN - executable program directory
 +
* HPC_{{uc:{{#var:app}}}}_LIB - library directory
 +
* HPC_{{uc:{{#var:app}}}}_INC - include file directory
 +
 
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
|}}
 
|}}
<!--PBS scripts-->
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<!--Job scripts-->
{{#if: {{#var: pbs}}|==PBS Script Examples==
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{{#if: {{#var: pbs}}|==Job Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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See the [[{{PAGENAME}}_Job_Sample_Scripts]] page for {{#var: app}} Job script examples.
 
|}}
 
|}}
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<!--Policy-->
 
<!--Policy-->
 
{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
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<!--Citation-->
 
<!--Citation-->
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
 +
===Serial Version===
 
If you publish research that uses {{#var:app}} you have to cite it as follows: <br/>
 
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.  
 
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.
 +
 
|}}
 
|}}
 
<!--Installation-->
 
<!--Installation-->

Latest revision as of 12:39, 12 August 2022

Description

Amber website  

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.

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).

Version

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.

Required Modules

Serial

For Amber 18:

  • intel/2017
  • amber/18

For amber 16:

  • intel/2018.1.163
  • amber

Example:

module load iintel/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

System Variables

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





Citation

Serial Version

If you publish research that uses Amber you have to cite it as follows:
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:

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.