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Version control of the Q molecular dynamics code version 5.7.
Q is a set of Molecular Dynamics (MD) tools tailored to specific kinds of free energy calculations, mainly:
Free Energy Perturbation (FEP)
Empirical Valence Bond (EVB)
Linear Interaction Energies (LIE)
The current makefiles make it relatively easy to compile the code in a linux or mac OSX environment.
You have to make sure first that gfortran is installed and if you want to compile the MPI version you also have to make sure that openmpi is installed.
If you're using gfortran make sure that you have version 4.8 or later. This applies both to compilation in mac and linux. To make sure that you have version 4.8 or later use:
gfortran --version
Right before issuing the "make" command.
To install in a linux environment you have to move to the src/ folder where the source code and the makefile are located at. To get information on how to use the makefile just type make in your terminal:
git clone https://github.com/qusers/qsource.git
cd qsource/src
make
Following the instructions for compilation using the gfortran compiler and the non-mpi version of the code would then take the form:
make all COMP=gcc
Or for MPI compilation (after loading a proper MPI compiler library):
make mpi COMP=gcc
To compile in Mac OSX 10.9.2 you can use native gfortran binaries which you can download from (https://gcc.gnu.org/wiki/GFortranBinaries#MacOS) or you can also compile using the GCC (Gnu Compiler Collection) distributions available to fink, macports or homebrew. In order to compile in a MAC you should call the fink environment first, usually with:
source /sw/bin/init.sh
alternatively, you can install homebrew and use (confirmed for Mac OSX 10.10):
brew install gcc
Then you proceed as in linux
git clone https://github.com/qusers/qsource.git
cd qsource/src
make all COMP=osx
This will take care of redirecting the binaries and object files to standard bin and obj folders for code tidyness.
After this you have to add the program to your system path by modifying your shell initiation script, that is, if your shell is bash, you can add the following lines to your .bashrc file using a text editor:
SOFT=/Users/johndoe/software
export QDIR=$SOFT/qsource
export PATH=$QDIR/bin:$PATH
Where $SOFT will be the place where your software folder is located at, e.g. /Users/johndoe/software
Once the q binaries are declared in your path you should be able to call all q binaries from your terminal. To test that the path to your compiled Q binaries has been correctly assigned you can issue the following commands in the terminal:
source .bashrc
echo $path | grep qsource
/Users/johndoe/software/qsource
qprep
###############################################################################
Welcome to Qprep version 5.7
Qprep>
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