Currently, my "job" is school. I am on a research assistant-ship pursuing a Ph.D. in physical organic chemistry. Part of my degree program has involved learning the "art" of computational chemistry / molecular modeling. Given the inherent toxicity in chemistry and my general aversion to odors, I really enjoy doing chemistry in silico. Having made a fairly substantial leap to a linux desktop has presented a number of challenges in this regard. First there has been the obvious struggle of losing some 'compatibility' with MS Office, but I believe this to now be a non-issue. The real struggle is continuing to use niche chemical software: Cambridgesoft's Chem3D, ChemDraw, E-Notebook; Wavefunction's Spartan; Gaussian's Suite of Programs including GaussView; SciFinder Scholar etc. Only Gaussian has a suitable linux version, but that has been difficult to obtain.
I have been mulling this problem over for nearly two-weeks and made several attempts at either finding a replacement software for each of the programs or otherwise attempting a "virtual" solution. I was able to install SciFinder in WINE which is a very nice "non-emulator." As mentioned before, I have found a few incomplete solutions for ChemDraw (BKChem, XDrawChem) and I now have tried a few different molecular GUIs including Viewmol, PyMol, Gabedit, and Tinker's Force Field Explorer (FFE). Pymol is powerful and has great aesthetic potential as a molecular viewer, but does not serve well as a molecular editor. Gabedit has lots of apparent functionality working as a front-end to a number of computational programs (G03, MOPAC, GAMESS, MOLPRO) but its editor is very clunky and lacks the intuitive feel I've grown accustomed to. Tinker and FFE I expect will eventually serve as a useful way to 'clean-up' structures with a force-field calculation, but it too has no builder!
After contacting support at PQS (a computational chemistry solutions company for hardware and software integrated in a parallel computing environment) I was given some advice to transfer the working GaussView install on the cluster computer (running Novell SUSE) to my Ubuntu 9.04 desktop. So far, that has not been a trivial task.
So somewhat at a loss, I have swallowed my new-found linux pride and installed XP on a virtual machine created through VirtualBox 3.0. This too required about 3 hours of research, trials and tribulations, but it seems to be the most powerful solution. There are lots of forums on the topic of this configuration, some of which are succinct and informative. Here are the links:
http://www.virtualbox.org/wiki/Downloads
http://download.virtualbox.org/virtualbox/3.0.0/UserManual.pdf
Supposedly it is possible to use VirtualBox to boot an existing OS installed on a partition of your HDD, but this requires a lot more understanding and caution and still has many bugs. Otherwise the process is quite straightforward:
1. Download and install VBox for your OS-distro
2. Create a Virtual Machine using the wizard: check the VBox Forums for discussions regarding set-up, configuring your virtual disk, etc:
3. Install a 'guest' operating system
4. Install "guest additions" from the 'Devices' drop-down menu of your window holding the guest OS
5. Set-up shared folders to allow file access between 'host' and 'guest'
That's as far as I am for now. I have installed most of the ChemOffice Suite (just need E-Notebook, and a key-crack) but still need GaussView and Spartan. The system runs quite fast, but I do have 4GB RAM on my 'host' and allocated 1024MB RAM for my 'guest.'
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