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This is nMoldyn-3.0.0, an interactive program for the analysis of Molecular Dynamics trajectories. This program is copyrighted but free to use for anyone under the CeCILL license, see the file LICENSE for details.

nMoldyn should work with all major variants of Unix, including Linux and MacOSX and Windows. There is little system-specific code in nMoldyn itself, so porting nMoldyn to other systems should be straightforward. However, we cannot provide any support for this.

If you have any questions about nMoldyn that are not answered on the Web page mentioned above, please contact the authors.

Eric Pellegrini Calcul Scientific Institut Laue Langevin 6 Rue Jules Horowitz 38042 Grenoble France E-Mail: pellegrini@ill.fr

Konrad Hinsen Centre de Biophysique Moleculaire (CNRS) Rue Charles Sadron 45071 Orleans Cedex 2 France E-Mail: hinsen@cnrs-orleans.fr

Gerald Kneller Centre de Biophysique Moleculaire (CNRS) Rue Charles Sadron 45071 Orleans Cedex 2 France E-Mail: kneller@cnrs-orleans.fr

Step 1: Prerequesites

Before installing nMOLDYN make sure that the following components are installed and configured properly:

-Tcl and Tk libraries version >= 8.4

-Python 2.4 or higher -numpy version >= 1.2 -matplotlib version >= 0.98 -pyro version >= 3.9 -Scientific version >= 2.8 -MMTK version >= 2.6.1

-NetCDF library version >= 3.6.1

To check for that, in a terminal, type

python -c 'import Scientific.IO.NetCDF'

If you get no error message NetCDF is likely to be properly installed and configured on your system.

Step 2: installation

In a terminal, type the following instructions in the directory where you untared the nMOLDYN archive:

cd nMOLDYN-3.X.Y python setup.py build python setup.py install

The last command may require administrator privileges.

Step 3: running nMOLDYN

Once the installation is completed run nMOLDYN by typing

./nMOLDYNStart.py

in your Python binaries directory.

In the future, you should create an alias/shortcut for that script in order to not disrupt any component of that sensitive directory.

WARNING:

If the version of Scientific used to run nMOLDYN is the 2.9.0, small changes has to be performed in order to use nMOLDYN in parallel mode via a Pyro server.

The changes are the following:

FILE : MasterSlave.py LOCATION: Scientific installation directory

REPLACE

def getMachineInfo():
import os sysname, nodename, release, version, machine = os.uname() pid = os.getpid() return "PID %d on %s (%s)" % (pid, nodename, machine)

BY

def getMachineInfo():
import os import platform sysname, nodename, release, version, machine, processor = platform.uname() pid = os.getpid() return "PID %d on %s (%s)" % (pid, nodename, machine)

If you are not familiar with the Python installed modules file structure, you can find the path for Scientific directory by running the following command within the Python interpreter:

import Scientific print Scientific.__path__[0]

KNOWN BUGS:

  • Bug with tk >= 8.5 on Linux (Fedora, Suse, Ubuntu): when using a tkMessageBox, if you click 'Yes'

the answer will be the same as 'No'! In nMOLDYN, you will experience this bug at the end of an analysis when you can decide to plot the results just after the analysis. Whatever is your decision ('Yes' or 'No'), no plot will be displayed.

Here is the proposed patch (http://bugs.python.org/issue4961):

--- Lib/lib-tk/tkMessageBox.py (revision 73494) +++ Lib/lib-tk/tkMessageBox.py (working copy) @@ -70,11 +70,13 @@

if title: options["title"] = title if message: options["message"] = message res = Message(**options).show()
  • # In some Tcl installations, Tcl converts yes/no into a boolean
  • # In some Tcl installations, yes/no is converted into a boolean. if isinstance(res, bool):
  • if res: return YES
  • if res:
  • return YES
return NO
  • return res
  • # In others we get a Tcl_Obj.
  • return str(res)
def showinfo(title=None, message=None, **options):
"Show an info message"