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acelab:gromacs

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acelab:gromacs [2015/09/02 12:13]
mcawood 		acelab:gromacs [2021/12/09 16:42] (current)
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 ===General Info=== ===General Info===
  
-GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids.+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.  It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.  [[http://www.gromacs.org/About_Gromacs|source]]
  
 ===Useful Links=== ===Useful Links===
  
-HPCAC Guide [http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf] \\ +HPCAC Guide [[http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf]] \\ 
-Acceleration and parallelization [http://www.gromacs.org/Documentation/Acceleration_and_parallelization]+Acceleration and parallelization [[http://www.gromacs.org/Documentation/Acceleration_and_parallelization]]
  
 ===Installation Guide=== ===Installation Guide===
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   export PATH=/home/$USER/GROMACS/gromacs-x86/bin:$PATH   export PATH=/home/$USER/GROMACS/gromacs-x86/bin:$PATH
  
-Test the installation by using the regression tests which ship with the release, available here: http://www.ace.chpc.ac.za/tars/regressiontests.tar.gz+Test the installation by using the regression tests which ship with the release, available here: [[http://www.ace.chpc.ac.za/tars/regressiontests.tar.gz|regressiontests.tar.gz]]
   cd ~/GROMACS/tests   cd ~/GROMACS/tests
   tar -xf Regressiontests.tar.gz   tar -xf Regressiontests.tar.gz
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