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--- acelab:gromacs [2015/09/01 15:43]
mcawood created
+++ acelab:gromacs [2021/12/09 16:42] (current)
@@ Line 1: / Line 1: @@
-==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===
   cd ~
@@ Line 47: / Line 47: @@
   sudo yum install blas-devel lapack-devel atlas-devel libxml2-devel
-===CMAKE===
+==CMAKE==
   cd ~/GROMACS/tars
@@ Line 57: / Line 57: @@
   make install
-===BINUTILS===
+==BINUTILS==
   cd ~/GROMACS/tars
@@ Line 67: / Line 67: @@
   make install
-===GROMACS===
+==GROMACS==
   cd ~/GROMACS/tars
@@ Line 76: / Line 76: @@
   cd build
-====x86 build====
+==x86 build==
   cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=off -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-x86/ -DGMX_BUILD_OWN_FFTW=ON -DGMX_BUILD_UNITTESTS=ON
@@ Line 82: / Line 82: @@
   make install
-====CUDA build====
+==CUDA build==
 The CUDA version requires a CUDA SDK of at least version 4.0, however the latest is recommended (version 7.0 was used for testing).  If the SDK in not found in the default /usr/local/cuda directory, then source it.
@@ Line 89: / Line 89: @@
   make install
-==Test Installation==
+===Test Installation===
 Source the GROMACS installation:
   export PATH=/home/$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
   tar -xf Regressiontests.tar.gz
@@ Line 100: / Line 100: @@
   ./gmxtest.pl -suffix _mpi all
-==Benchmark==
+===Benchmark===

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