Chembytes Virtual Project: a linux appliance for VMware

Finally I have found the time to create a brand new linux vmware/fusion virtual appliance for computational chemistry. I chosen to create the appliance for vmware because there is wonderful free player for Windows and linux, and the appliance will run also on mac os x if you have Fusion. For the moment I will not convert this appliance for virtualbox, nor I plan to create a new one for virtualbox. Sorry.

The Chembytes virtual appliance

This appliance is based on Ubuntu 9.10 (32-bits) and is fully updated at the present (November, 22nd 2009). The vmware tools are not installed, so to let you install the version you want; the tools can also be installed using the new version of VMPlayer 3.0. I know many computers now are 64-bits, so I'm working to an equivalent appliance but with the kernel 64-bits.


This virtual appliance has 20gb of HD as maximum (virtualized by using 2gb files, so to be used on FAT32 partitions), ethernet (NAT or Bridge or host only), a cd rom, usb on demand and 512MB of ram. The following keyboard layouts are installed: Italian, United Kingdom, France and Belgium, but the layout for the default screen is italian. You can change the keyboard layout at the login screen using the menu' at the bottom or by editing the file /etc/default/console-setup as sudo.
Please remember to install the VMware Tools.

20gb are not enough for you? Well, here you can download a virtual hard disk of 50gb (the actual size of the file is only 6MB) and then mount it in the virtual machine as a second hard disk. You will need to edit the configuration file of the virtual machine.
You can also use the latest version of VMPlayer, that allows to change many setting for the virtual machine.

Default User

The default user for the appliance is chemuser, and the password is chemuser (you may want to change it ASAP). By default,there is no automatic login.


People in my lab can downloaded it from mn-cmn in the directory sharecmn\andrea\VirtualLinux. Also the players for Linux and Windows are there.

If you have no access to the server listed above, you can download for free the application from my Adrive space. Click [* here]

Installed software

I have installed quite a lot useful software.


MENDELEY: Like Itunes, but for papers.

GABEDIT: graphical user interface to Ab Initio packages.
Gabedit is a graphical user interface to computational chemistry packages like the Free Software package MPQC. Other (proprietary) packages supported include:
- Gaussian
- Molcas
- Molpro
- Q-Chem
running locally or on a remote server (supporting FTP, RSH and SSH). It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.


GNUPLOT: A command-line driven interactive plotting program

Gnuplot is a portable command-line driven interactive data and function plotting utility that supports lots of output formats, including drivers for many printers, (La)TeX, (x)fig, Postscript, and so on. The X11-output is packaged in gnuplot-x11.

Data files and self-defined functions can be manipulated by the internal C-like language. Can perform smoothing, spline-fitting, or nonlinear fits, and can work with complex numbers.

XMGRACE: An XY plotting tool

Grace is a point-and-click tool that allows the user to draw X-Y plots. This is the program formerly known as Xmgr.
A few of its features are: User defined scaling, tick marks, labels, symbols, line styles, colors. Polynomial regression, splines, running averages, DFT/FFT, cross/auto-correlation. Batch mode for unattended plotting. Hardcopy support for PostScript, FrameMaker and several image

MM/MD Simulation packages

GROMACS: Molecular dynamics simulator, with building and analysis tools

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 and lipids 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.

TINKER: The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Merck Molecular Force Field (MMFF), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

Desktop publishing and graphical applications

LATEX: TeX Live: Basic LaTeX packages

These packages are either mandated by the core LaTeX team, or otherwise highly recommended.

This package includes the following CTAN packages:
ae — Virtual fonts for PDF-files with T1 encoded CMR-fonts.
amscls — The amscls package.
amsltx2 — The amsltx2 package.
amsmath — The amsmath package.
amsrefs — The amsrefs package.
babel — Multilingual support for Plain TeX or LaTeX.
babelbib — Multilingual bibliographies.
carlisle — Miscellaneous small packages by David Carlisle.
colortbl — The colortbl package.
fancyhdr — Extensive control of page headers and footers in LaTeX2e.
geometry — Flexible and complete interface to document dimensions.
graphics — No caption.
hyperref — Extensive support for hypertext in LaTeX.
latex — the basic LaTeX package.
latex-fonts — The latex-fonts package.
latexconfig — The latexconfig package.
ltxmisc — Miscellaneous LaTeX styles.
mfnfss — Packages to typeset oldgerman and pandora fonts in LaTeX.
natbib — Flexible bibliography support.
pdftex-def — The pdftex-def package.
pslatex — Use PostScript fonts by default.
psnfss — Font support for common PostScript fonts.
pspicture — The pspicture package.
tools — The tools package.
bin-latex — the basic LaTeX binary package.


gfortran: g95 compiler

Fortran compiler (installed version 4.2 (linked by gfortran) , 4.3 and 4.4)

python-numpy: Numerical Python adds a fast array facility to the Python language

Numpy contains a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities.
Numpy replaces the python-numeric and python-numarray modules which are now deprecated and shouldn't be used except to support older software.

Software I have not installed, but you may want to

  • ipython (interactive python idle)
  • Octave (similar to matlab and mathematica)
  • Wine (windows emulator for windows software)
  • Molden
  • Gdis


How to install Molden

In order to install the recent precompiled binary of Molden, you need to install libg2c. To do this, add in synaptic the following repository:

deb hardy universe

How to install G77

To install g77, add in synaptic the following repository:

deb hardy universe
sudo aptitude install g77

Beware that this could downgrade some libraries

Mount a windows share directory

You can mount a windows share directory in nautilus using "connect to server" from the Places menu. This will allow you to browse the director, copy/modify and delete files. Unfortunately, this works more like a ftp connections and the files in that directory will not available directly in any application, e.g. with file -> open. If you need this, you have to mount the windows share directory in a destination directory in your hard disk, e.g. remote_dir, as following:

mkdir remote_dir
sudo mount -t smbfs -o username=your_user_name,password=your_password //server/share/dir remote_dir

You need to install the package smbfs with synaptic or apt-get. And remember to properly unmount the file system.

Where to find my real desktop

In the virtual machine settings (VM\Settings\options), Shared Folder option have to be Enabled. The path to the Shared Folder in the virtual machine is /mnt/hgfs/

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