--- /dev/null
+GROMACS is free software, distributed under the GNU General Public License.
+The GROMACS-GPU release however includes / relies on code covered by several
+different licences as described below.
+
+
+1. GROMACS source
+
+The major parts of the GROMACS source are covered by the GNU General Public
+License, a copy of this license can be found in the file COPYING.
+
+
+2. The memtestG80 library
+
+The memtestG80 library written by Imran Haque is Copyright 2009, Stanford University,
+covered by the LGPL license and may be used under the following terms:
+
+IN NO EVENT SHALL STANFORD UNIVERSITY BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF STANFORD UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+STANFORD UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOTLIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION PROVIDED HEREUNDER IS PROVIDED "AS IS". Folding@home HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+
+Restrictions:
+
+You may use this software on a computer system only if you own the system or have the written permission of the owner.
+
+You may not alter the software or associated data files.
+
+Certain builds of this software incorporate by linkage code from the libintl
+and libiconv libraries, which are covered by the Library GNU Public License,
+available at http://www.gnu.org/licenses/lgpl-3.0.txt.
+
+
+3. OpenMM (binary distributions only)
+
+There are several licenses which cover different parts of OpenMM as described
+in the file openmm/licenses/Licenses.txt accompanying the binary discribution.
+
+
+4. FindCUDA.cmake script
+
+The FindCUDA.cmake script may be used under the terms of the MIT License:
+
+ James Bigler, NVIDIA Corp (nvidia.com - jbigler)
+ Abe Stephens, SCI Institute -- http://www.sci.utah.edu/~abe/FindCuda.html
+
+ Copyright (c) 2008 - 2009 NVIDIA Corporation. All rights reserved.
+
+ Copyright (c) 2007-2009
+ Scientific Computing and Imaging Institute, University of Utah
+
+ This code is licensed under the MIT License. See the FindCUDA.cmake script
+ for the text of the license.
\ No newline at end of file
- Welcome to GROMACS 3.1!
+ Welcome to GROMACS!
Note: Detailed, step-by-step installation instructions
are available on the website http://www.gromacs.org .
* SHORT INSTRUCTIONS FOR THE IMPATIENT:
-Starting with version 3.0, the GROMACS compile and install procedure
-was changed to simplify things for you. We now use a standard
-autoconf script and makefiles created by automake, like most
-GNU programs. This means your normal installation actions are
-limited to:
+GROMACS uses a standard autoconf script and makefiles created
+by automake, like most GNU programs. This means your normal
+installation actions are limited to:
./configure
make
--- /dev/null
+
+ Welcome to GROMACS-GPU!
+
+Note: Detailed, step-by-step installation instructions as
+well as additional information are available on the website
+http://www.gromacs.org/gpu
+
+
+* INSTALLING FROM BINARY DISTRIBUTION:
+
+0. Prerequisites:
+ • OpenMM (included in the binary release)
+ • NVIDIA CUDA libraries (version >=3.0);
+ • NVIDIA driver (for details on compatiblity consult
+ http://www.nvidia.com/Download/index5.aspx);
+ • NVIDIA CUDA-enabled GPU (for compatiblity list see
+ http://www.gromacs.org/gpu).
+
+
+1. Download and unpack the binary package for the respective
+OS and architecture. Copy the content of the package to your
+normal GROMACS installation directory (or to a custom location).
+Note that as the distributed Gromacs-GPU packages do not contain
+the entire set of tools and utilities included in a full GROAMCS
+installation. Therefore, it is recommended to have a ≥v4.5
+standard Gromacs installation along the GPU accelerated one.
+e.g. on unix:
+
+tar -xvf gromacs-4.5-GPU.tar.gz
+cp -R gromacs-4.5-GPU/* PATH_TO_GROMACS_INSTALLATION
+
+
+2. 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.
+
+
+3. 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
+
+
+4. 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.
+
+
+
+* INSTALLING FROM SOURCE DISTRIBUTION:
+
+GROMACS-GPU uses a cmake build-generator and makefiles on unix.
+This means your normal installation actions are limited to:
+
+cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
+make mdrun
+make install-mdrun
+
+
+
+* ARE YOU STILL HAVING PROBLEMS?
+
+Post it to the GROMACS mailing lists. We read these on a regular basis,
+and in many cases another user might already be familiar with the
+task you're trying to perform!
Welcome to the official version of GROMACS!
-There are no significant changes to the installation or use between version
-3.1 and 3.0, so if you're already used to 3.0 you can just go ahead and update.
-A lot of things changed with version 3.0, though. Not only is the code
-significantly faster, but we also introduced a completely new installation
-process and licensed the package under the GPL (see the COPYING file).
-
If you are familiar with unix, it should be fairly trivial to compile and
install GROMACS. Installation instructions are available in the INSTALL file,
and a more extended step-by-step guide can be found on http://www.gromacs.org .
included in the main distribution. We'll be happy to consider any decent
code. If it's a separate program it can probably be included in the contrib
directory straight away (not supported by us), but for major changes in the
-main code we appreciate if you first test that it works with MPI,
-double precision, fortran code, etc.
+main code we appreciate if you first test that it works with (and without)
+MPI, threads, double precision, etc.
If you still want to distribute a modified version or use part of GROMACS
in your own program, remember that the entire modified must be licensed
H.J.C. Berendsen, D. van der Spoel and R. van Drunen
Comp. Phys. Comm. 91, 43-56 (1995)
-* GROMACS 3.0: A package for molecular simulation and trajectory analysis
- Erik Lindahl, Berk Hess and David van der Spoel
- J. Mol. Mod. 7, 306-317 (2001)
+* GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
+ molecular simulation
+ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
+ J. Chem. Theory Comput. 4 (2008) pp. 435-447
There are a lot of cool features we'd like to include in future versions,
but our resources are limited. All kinds of donations are welcome, both in
--- /dev/null
+
+ Welcome to the official version of GROMACS-GPU!
+
+
+GROMACS-GPU provides GPU-accelerated MD simulations.
+The current release uses the OpenMM library.
+
+This is a first beta release and therefor it is targeted at developers
+and advanced users and is NOT intended for production use.
+
+Installation instructions are available in the INSTALL-GPU file.
+More details on the GPU accelerated release are available on the
+GROMACS-GPU website: http://www.gromacs.org/gpu.
+
+Also see the README file for general GROMACS information.
+
+ * * * * *
+
+GROMACS is free software, distributed under the GNU General Public License.
+The GROMACS-GPU release however includes / relies on code covered by several
+different licences. For details see the COPYING-GPU file.
\ No newline at end of file
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff