[ale] Stress, via RH8 and confusion

[Dow Hurst]

I'll help you out on the chemistry software.  The most interesting to me 
right now to check out is http://www.molsoft.com
 and the demo for linux.  Haven't tried it yet.  Xdrawchem and Xykron 
are cool programs that came with SuSE 8.1.  Rasmol is very popular for 
viewing Protein Data Bank files.  There aren't too many fullblown 
programs with pretty GUIs and most are expensive that I am aware of.  
EMBOSS is a nice set of tools for bioinformatics that is free.  It 
depends on what you want to do as to what is available for you.  Chime 
will let you look at PDB files thru a browser.  Maybe VMD and NAMD would 
be the most powerful for you without cost.  They will work together, 
however, I am not sure if you can create structures but only manipulate 
precreated structures.  Just google VMD and/or NAMD to get to the 
Theoretical Biophysics group's homepage where you can get the software.  
NAMD and Gromacs are the fastest calculation software for molecular 
dynamics on clusters right now.
Dow

tfreeman at intel.digichem.net wrote:

>Please be warned: this rambles. I appologise for the relative waste 
>of you bandwidth. Delete without reading
>
>OK. You made it this far, I guess that you aren't interested in free 
>advice. 8-)
>
>By way of some background, I've been using Red Hat since sometime around 
>RH3.?, because they were the first to successfully configure my printer. 
>In the years since, I've gotten pretty used to the RH way, although I've 
>looked at SuSe, Debian, Slackware, Yellow Dog, and Mandrake along the way 
>with variable degrees of success.
>
>I picked up a new machine to serve as an experimental machine & 
>compile toy (this is the first one I've owned to break 1GHz processor 
>speed). I started out trying RH7.3 on this machine, but the video refused 
>to configure past 800x600 or so. I broke down, obtained RH8.0, installed, 
>and got the same results. I had a Radion 7000 which I had tried in another 
>machine without great joy, so I plugged that in and got the resolution 
>1024x768 (or whatever) I want. 
>
>Fix one challenge, two more want to show up. I will agree with Red Hat that 
>the Bluecurve desktop is attractive in many respects, but I don't like it 
>and don't much want to keep it. Additionally, the menus have gone from 
>long to _much_lloonnggeerr_, which I also dislike. I also note that 
>two/three applications I rather liked in the past have fallen off the 
>distribution. These issues can eventually be dealt with obviously - this 
>is Linux, and RH hasn't made it significantly harder to work from that 
>reality.
>
>This may be my opportunity to at least try Gentoo, and before I fix this 
>machine up I may choose to do so. I haven't guessed/decided on that yet.
>
>What I appear to want to do is utilize a base distribution (RH by bias), 
>and rip out the annoyances so as to replace them with "good" stuff. When/if 
>things stabilize on the experimental box, then migrate the "good" stuff 
>out to the other boxen. I realize that apt-get has many adherents, and 
>may fit slightly better with my needs, but isn't too horridly shabby at 
>this point either. In my hands, and at this time, rpm _does_ grossly 
>interfere with the ripping out/replacing/modifying step in the middle, 
>where recompiling almost everything makes a fair amount of sense.
>
>I've got a horrid feeling that what I want is a Gentoo/Red Hat hybrid 
>distribution with most of the rough edges filed off so I don't leave as 
>many finger tips behind after cutting self in the process. Plus, some way 
>of at least semi-automating the updates process for security headaches, 
>not that a personal playground should have as many security issues as the 
>professional environment. (I think I can trust me with respect to security 
>breaches 8-))
>
>If I'm asking a question here, I cann't tell what it is. I might be just 
>venting frustration with being lazy, and wanting to go in a direction I 
>don't see a commercial carrier to take me there. 
>
>What are the "I wants"?
>  I want to look at Gnome2.2(?) natively
>  I want to look at the latest KDE natively
>  I want to try openMosix as a cluster environment for desktop use
>  I want to upgrade a card/subsystem, and not upgrade the whole system 
>         software package
>  I want a girl friend who understands how to guard my back in the dark 
>         alleys of life (ok, not linux)
>  I want some training on chemical structure software where I can _afford_ 
>         the cost of the software. (Chemistry is my background, although 
>         for a number of reasons I've been reduced more to hobby 
>         interest and involvement.) I somehow doubt that the vendors 
>         are going to help me out here!
>
>I could be silly and keep going, but I've imposed on the good graces of 
>the list enough here. Especially since I _still_ don't know the question I 
>should be asking
>
>Thanks for listening, and allowing me the bandwidth.
>
>  
>

-- 
__________________________________________________________
Dow Hurst                  Office: 770-499-3428
Systems Support Specialist    Fax: 770-423-6744
1000 Chastain Rd. Bldg. 12
Chemistry Department SC428  Email:   dhurst at kennesaw.edu
Kennesaw State University         Dow.Hurst at mindspring.com
Kennesaw, GA 30144
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