Difference between revisions of "AMBER"
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine:pbs| | + | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> |
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
| Line 25: | Line 25: | ||
== Version == | == 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=== | ||
| − | * intel/ | + | |
| + | '''For Amber 18:''' | ||
| + | |||
| + | * intel/2017 | ||
| + | *amber/18 | ||
| + | |||
| + | '''For amber 16: | ||
| + | ''' | ||
| + | * intel/2018.1.163 | ||
* amber | * amber | ||
| + | |||
Example: | Example: | ||
| − | module load | + | module load iintel/2017 amber/18 |
===Parallel (MPI)=== | ===Parallel (MPI)=== | ||
| − | * intel/ | + | |
| − | * openmpi | + | '''For amber 18''' |
| + | |||
| + | * intel/2017 | ||
| + | *openmpi/3.1.2 | ||
| + | *amber/18 | ||
| + | |||
| + | '''For amber/16:''' | ||
| + | |||
| + | * intel/2018.1.163 | ||
| + | * openmpi/3.0.0 | ||
* amber | * amber | ||
| − | module load intel/ | + | Example: |
| + | module load intel/2017 openmpi/3.1.2 amber/18 | ||
| − | ===GPU ( | + | ===GPU (Parallel/MPI)=== |
| − | |||
| − | |||
| − | |||
| − | + | For amber 18: | |
| − | + | * cuda/9.2.88 | |
| − | * intel/ | + | * intel/2017 |
| − | * openmpi | + | * openmpi/3.1.2 |
| − | + | * amber/18 | |
| − | * amber/ | ||
| − | module load intel/ | + | Example: |
| + | module load cuda/9.2.88 intel/2017 openmpi/3.1.2 amber/18 | ||
==System Variables== | ==System Variables== | ||
* AMBERHOME | * AMBERHOME | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable program directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_LIB - library directory |
| + | * HPC_{{uc:{{#var:app}}}}_INC - include file directory | ||
<!--Configuration--> | <!--Configuration--> | ||
| Line 73: | Line 88: | ||
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY | WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY | ||
|}} | |}} | ||
| − | <!-- | + | <!--Job scripts--> |
| − | {{#if: {{#var: pbs}}|== | + | {{#if: {{#var: pbs}}|==Job Script Examples== |
| − | See the [[{{PAGENAME}} | + | 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== | ||
Revision as of 21:16, 6 December 2019
Description
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.