[gmx-users] how to install the gromacs-4.5.5 with the gpu on the linux

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 4 17:24:14 CEST 2011

On 5/10/2011 2:10 AM, 杜波 wrote:
> i see the instructions on the web:
> Installing
> Download and unpack the binary package for the respective OS and

You are instructed to get a binary package. However, above this text is 
an updated set of instructions that declares the binary packages are 
deprecated. Whoever did the update to this page expected you to read all 
of the text, unfortunately.

> architecture. Copy the content of the package to your normal Gromacs
> installation directory (or to a custom location). Note that the
> distributed Gromacs-GPU packages do not contain the entire set of
> tools and utilities included in a full Gromacs installation.
> Therefore, it is recommended to have a ≥v4.5 standard Gromacs
> installation along the GPU accelerated one.
> Add the openmm/lib directory to your library path, e.g. in bash:
> export LD_LIBRARY_PATH=path_to_gromacs/openmm/lib:$LD_LIBRARY_PATH
> If there are other OpenMM versions installed, make sure that the
> supplied libraries have preference when running mdrun-gpu. Also, make
> sure that the CUDA libraries installed match the version of CUDA with
> which Gromacs-GPU is compiled.
> Set the OPENMM_PLUGIN_DIR environment variable to contain the path to
> the openmm/lib/plugins directory, e.g. in bash:
> export OPENMM_PLUGIN_DIR=path_to_gromacs/openmm/lib/plugins
> At this point, running the command path_to_gromacs/bin/mdrun-gpu -h
> should display the standard mdrun help which means that the binary
> runs and all the necessary libraries are accessible.
> and download the gromacs-4.5.5.tar.gz on the http://www.gromacs.org/Downloads,

This is a package of source code. If you read further on the page, there 
are instructions for building from the source code. You will need to 
consult the regular install-from-source instructions also.

> and then unpack it, but i not find the file openmm!
> how can i do, if i want to install  gromacs-4.5.5 with the gpu on the
> linux ?thanks!
> Bo Du
> Department of Polymer Science and Engineering,
> School of Chemical Engineering and technology,
> Tianjin University, Weijin Road 92, Nankai District 300072,
> Tianjin City P. R. China
> Tel/Fax: +86-22-27404303
> E-mail: 2008dubo at gmail.com

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