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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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|1}}            <!--PBS SCRIPTS-->
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|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
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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).  
 
== Version ==
 
The default version of Amber is ''Amber 12''.  ''Amber 11'' is also available via ''module load amber/11''.  If you are still using ''Amber 11'', you should switch to ''Amber 12'' as soon as you can.
 
 
The version for the latest installation is: Amber 12.21 and AmberTools 13.23
 
  
 
<!--Modules-->
 
<!--Modules-->
 
==Required Modules==
 
==Required Modules==
 +
For more details on specific modules required for different versions of AMBER, run <code>module spider amber</code>
 +
 +
{|cellpadding="10"
 +
|-style="vertical-align:top;"
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|
 
===Serial===
 
===Serial===
* intel/2013
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 +
'''For Amber 18:'''
 +
 
 +
* intel/2017
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*amber/18
 +
 
 +
'''For amber 16:
 +
'''
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* intel/2018.1.163
 
* amber
 
* amber
 +
 +
Example:
 +
module load intel/2017 amber/18
 +
||
 
===Parallel (MPI)===
 
===Parallel (MPI)===
* intel/2013
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* openmpi
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'''For amber 18'''
 +
 
 +
* intel/2017
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*openmpi/3.1.2
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*amber/18
 +
 
 +
'''For amber/16:'''
 +
 
 +
* intel/2018.1.163
 +
* openmpi/3.0.0
 
* amber
 
* amber
===GPU (Serial)===
+
 
* intel/2013
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Example:
* cuda
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module load intel/2017 openmpi/3.1.2 amber/18
* amber/12-cuda
+
||
 
===GPU (Parallel/MPI)===
 
===GPU (Parallel/MPI)===
* intel/2013
 
* openmpi
 
* cuda
 
* amber/12-cuda
 
  
 +
For amber 18:
 +
 +
* cuda/9.2.88
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* intel/2017
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* openmpi/3.1.2
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* amber/18
 +
 +
Example:
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module load cuda/9.2.88 intel/2017 openmpi/3.1.2 amber/18
 +
|}
 
==System Variables==
 
==System Variables==
 
* AMBERHOME
 
* AMBERHOME
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable program directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable program directory
* HPC_{{#uppercase:{{#var:app}}}}_LIB - library directory
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* HPC_{{uc:{{#var:app}}}}_LIB - library directory
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* HPC_{{uc:{{#var:app}}}}_INC - include file directory
  
 
<!--Configuration-->
 
<!--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.
 
|}}
 
|}}
 
<!--Policy-->
 
<!--Policy-->

Latest revision as of 20:09, 5 February 2024

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).

Required Modules

For more details on specific modules required for different versions of AMBER, run module spider amber

Serial

For Amber 18:

  • intel/2017
  • 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

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.