From owner-chemistry@ccl.net Thu Dec 14 02:36:01 2006 From: "Daniel Jana dfjana:+:gmail.com" To: CCL Subject: CCL: Linux for dual dual-core machines Message-Id: <-33251-061214023101-9501-lOoBmwHePe0LzTpODSHIFQ]![server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 14 Dec 2006 08:30:58 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana]![gmail.com] Darryl Reid darryl.reid(~)gmail.com wrote: > To get the maximum performance > out, you have to go the "hard" way and compile a kernel optimized for > Opteron, Which should be normal routine anyway... at least for a system that is going to be used in calculations. There is so much "garbage" that comes with the kernel... > or better yet, compile every package that way, e.g. install a > source-based distribution like Gentoo fully customized for the specific > hardware. Well, this would be a very nice discussion... I've read arguments about this for every possible side of the matter. There should be a performance gain, for sure, but the fact is you spend some (computational) time compiling (or, in Gentoo talk, emerging) the programs. In the other case, it's much faster as it's just as unzipping a file. So, the speed you gain, in the end might be lost if you count with the time you spent emerging the program. You get one good thing though. There won't be surprises like "Oh, I have this installed!" if it is there, you put it... I'm a Gentoo user myself and work with SuSE in a cluster. Although I still prefer Gentoo, I don't know if I'd use it in a cluster (which means I'd probably stay with SuSE). Overall it's been a fantastic distribution for me. > However, be warned that installing Gentoo is far more complicated > and requires some low level tinkering and configuration file editing than > installing Mandriva (which is very easy plug-n-play requires only a few > mouse > clicks). > Used to be harder. By the early stages, when you part of the recommended installation procedure was starting from scratch you could lose some time (which meant days, in the old hardware I was trying it) until you had a system at all. Right now the installation procedure takes you to a point where you have a functional system by a short time and then, if you really want it you can start rebuild the system. So, even a beginner should be able to make it :) Daniel Jana From owner-chemistry@ccl.net Thu Dec 14 11:28:01 2006 From: "Daniil Bratashov dn2010(-)gmail.com" To: CCL Subject: CCL: Linux for dual dual-core machines Message-Id: <-33252-061214034545-3045-dUrFERp/aEfNhmUYT4fk1g^_^server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 14 Dec 2006 10:41:02 +0300 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010,gmail.com] On Wed, 13 Dec 2006 13:07:26 -0500 "John McKelvey jmmckel|-|gmail.com" wrote: > Could is ask what flavor of Linux should work best with an Asus > K8N-DL with dual dual-core AMD Opterons? [160 Gbyte NCQ Seagate SATA2 > drive... more to be added.. want to get the machine running first; > 2Gbyte memory] Every major distribution nowadays has official or unnoficial x86_64 version. Look at distrowatch.com for more info. And don't forget, the best distribution is distribution, which used by your local linux guru. As general recomendation RHEL and its clones (CentOS, whitebox, scientific) and Novell SUSE (SLES/SLED) are best commercial distro, Fedora, OpenSUSE, Ubuntu and Debian as community binary distro and Gentoo as source one. Slamd64 is version of Slackware for x86_64. Don't blame me if I forgot something. What to look for is another question. If you need 32bit emulation for workstation not all distro have it. Some problems are in using ACML as system BLAS and LAPACK, and so on. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Thu Dec 14 12:02:00 2006 From: "Russell Glavey russellglavey .. hotmail.com" To: CCL Subject: CCL: Atom types and parameters for tetrolic acid when using amber Message-Id: <-33253-061214085813-11101-+jwElLoNYQL+a3XGZlINCw(_)server.ccl.net> X-Original-From: "Russell Glavey" Date: Thu, 14 Dec 2006 08:58:13 -0500 Sent to CCL by: "Russell Glavey" [russellglavey_._hotmail.com] Dear CCL Subscribers, I am presently using amber, (for the first time) to model tetrolic acid. I have a number of queries relating to my attempt 1: What is the most appropriate atom type for the sp2 carbon single bonded to one oxygen and one carbon and double bonded to an oxygen. I have chosen the C atom type. 2: What is the most appropriate atom type for the sp carbon single bonded to one carbon and triple bonded to another carbon. I have chosen CM. 3: What is the most appropriate choice for the oxygen in the carboxyilic acid that is double bonded to a carbon atom. I have chosen 02. 4: What are the most appropriate angle parameters for the 0H-C-O2 and OH-C-CM bond angles and what literature can they be sourced in. Thank you in advance for your assistance. Russell Glavey russellglavey###hotmail.com From owner-chemistry@ccl.net Thu Dec 14 12:44:01 2006 From: "Igor Filippov Contr igorf]_[helix.nih.gov" To: CCL Subject: CCL:G: Linux for dual dual-core machines Message-Id: <-33254-061214121608-21960-Nhfj0TOPKwmJ37usGVcJzQ,,server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 14 Dec 2006 12:15:54 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf=-=helix.nih.gov] > To get the maximum performance > out, you have to go the "hard" way and compile a kernel optimized for > Opteron, > Which should be normal routine anyway... at least for a system that is > going to be used in calculations. There is so much "garbage" that comes > with the kernel... Great advice! Then your Gaussian/Jaguar/PipelinePilot/Whatever other software you're using stops working, you make a call to Gaussian/Schrodinger/Accelrys/Whoever and find out that your hand- crafted kernel is not on the list of supported configurations. Surprise ! Check what your software needs are and choose a distribution based on that. No matter how amazing the performance gains could be, they would mean little if your software doesn't work. > Just keep in mind that multi-cpu systems need to have the CPU > frequencies synced, but I suppose you already knew that. After working with various computer systems for close to 10 years I never had to make sure that "CPU frequencies are synced" in an SMP system. I can't believe I've been missing that all this time... Come to think of it - how would you even begin to configure a computer with two or more CPUs to have them running at different clock speed ? And even more "curiouser" - for what possible purpose ? Igor From owner-chemistry@ccl.net Thu Dec 14 14:41:01 2006 From: "Daniel Jana dfjana(-)gmail.com" To: CCL Subject: CCL: Linux for dual dual-core machines Message-Id: <-33255-061214143918-29458-PX4v3C/TQ73VJoZ2nhSmPw:+:server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 14 Dec 2006 20:39:00 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana|-|gmail.com] Igor Filippov Contr igorf]_[helix.nih.gov wrote: >> Just keep in mind that multi-cpu systems need to have the CPU >> frequencies synced, but I suppose you already knew that. >> > > After working with various computer systems for close to 10 years I > never had to make sure that "CPU frequencies are synced" in an SMP > system. I can't believe I've been missing that all this time... > Come to think of it - how would you even begin to configure a computer > with two or more CPUs to have them running at different clock speed ? > And even more "curiouser" - for what possible purpose ? > Yes, I thought also it would be automatically done, but I came recently upon a post (sorry, can't find it anymore) on which there was a problem and the /var/log/messages stated something like "error, out of sync" or something. The point is not choosing different clock speeds is that they just vary slightly every time you boot (at least, my old P3 where I checked this did). Slight variations in that case are not problematic (less than .1% of the speed whenever I checked) but since the SMP systems need to be synced... I never run into that problem also but it was specifically for a dual core, dual cpu system and I'm still to deal with one of those. Soon, I hope... Daniel Jana From owner-chemistry@ccl.net Thu Dec 14 16:21:01 2006 From: "Mark Zottola mzottola],[gmail.com" To: CCL Subject: CCL:G: Potential Energy Surface Scans Message-Id: <-33256-061214143405-28865-URBrw1KF/OROkt16EolfrQ-$-server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_116664_7573585.1166121208872" Date: Thu, 14 Dec 2006 13:33:28 -0500 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola:-:gmail.com] ------=_Part_116664_7573585.1166121208872 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline I am investigating a system with several second order saddle points. One of the saddle points is a linear molecule with 2 degenerate imaginary frequencies. While this is a second order saddle point, it is effectively connecting the same reactant and product (or so I currently believe). In trying to validate that last assertion, I have been trying to perform a reaction coordinate calculation. However, when I use the keyword IRC with Gaussian03, I find that the degenerate modes causing the calculation to fail. Other than significantly deforming the transition state structure along one of the imaginary modes and minimizing to a ground state structure, is there any other way of validating which structures are connected via a transition state? As I mentioned, I am using Gaussian. Due to budgetary constraints, any other recommended package would have to be freeware and able to run on Linux. Thanks for any help! Mark ------=_Part_116664_7573585.1166121208872 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
I am investigating a system with several second order saddle points.  One of the saddle points is a linear molecule with 2 degenerate imaginary frequencies.  While this is a second order saddle point, it is effectively connecting the same reactant and product (or so I currently believe).
 
In trying to validate that last assertion, I have been trying to perform a reaction coordinate calculation.  However, when I use the keyword IRC with Gaussian03, I find that the degenerate modes causing the calculation to fail.  Other than significantly deforming the transition state structure along one of the imaginary modes and minimizing to a ground state structure, is there any other way of validating which structures are connected via a transition state?
 
As I mentioned, I am using Gaussian.  Due to budgetary constraints, any other recommended package would have to be freeware and able to run on Linux.
 
Thanks for any help!
 
 
Mark
------=_Part_116664_7573585.1166121208872-- From owner-chemistry@ccl.net Thu Dec 14 21:22:00 2006 From: "Sidney R. Santana santanasidney]*[yahoo.com.br" To: CCL Subject: CCL: Intramolecular Hydrogen Bonds: AIM vs GIAO NMR Message-Id: <-33257-061214212025-16272-JNfsBtS0GKXNRP8Fscb4Qg=-=server.ccl.net> X-Original-From: "Sidney R. Santana" Date: Thu, 14 Dec 2006 21:20:24 -0500 Sent to CCL by: "Sidney R. Santana" [santanasidney*yahoo.com.br] Dear CCL Users, I am studying a system with a intramoleculecular hydrogen bonds assigned by AIM. But, It is possible to attain the same, or similar, assignment with GIAO NMR calculations by a shielding and deshielding analysis. Please, I would appreciate to read some point views about it. Best Regards, Sidney R. Santana santanasidney_at_yahoo.com.br From owner-chemistry@ccl.net Thu Dec 14 22:21:00 2006 From: "Andrew D. Fant fant]^[pobox.com" To: CCL Subject: CCL:G: Linux for dual dual-core machines Message-Id: <-33258-061214215645-2870-iQxPgXDRzfKlGSZdoJwfMA]-[server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 14 Dec 2006 21:56:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant * pobox.com] Igor Filippov Contr igorf]_[helix.nih.gov wrote: > Sent to CCL by: "Igor Filippov [Contr]" [igorf=-=helix.nih.gov] >> To get the maximum performance >> out, you have to go the "hard" way and compile a kernel optimized for >> Opteron, >> Which should be normal routine anyway... at least for a system that is >> going to be used in calculations. There is so much "garbage" that comes >> with the kernel... > > Great advice! Then your Gaussian/Jaguar/PipelinePilot/Whatever other > software you're using stops working, you make a call to > Gaussian/Schrodinger/Accelrys/Whoever and find out that your hand- > crafted kernel is not on the list of supported configurations. > Surprise ! > > Check what your software needs are and choose a distribution based on > that. No matter how amazing the performance gains could be, they would > mean little if your software doesn't work. As someone who juggles these kind of issues for my job on a regular basis, I disagree. On the last cluster we set up, I took all the applications we were expected to run and made a matrix of the supported Linux distributions. In the end, there were none that were officially supported by all the vendors. And what do you do when the latest security patch, which is mandated by your facility NOC to maintain connection to the LAN and Internet is a "non-supported configuration"? Pick whichever current and currently supported distro you feel you are most comfortable with and can be most productive with, and stick to your guns with the vendors. Of course you know to cross-validate your results after any major upgrade anyway or system migration anyway, and with only one exception, I've found the ISV's to be willing to at least hear the problem and try to help with the proviso that they can drop the problem if it really IS your distribution not working. I've even have a couple ask for information about Gentoo when they find out that I am using it so that they can better support it, because they know that people do use it. In any case, most Linux vendors with clue ship a mixture of static binaries and their own shared object tree for anything that is beyond the LSB spec. I've actually had more problems with them shipping too many shared libraries that my system already provides than my not having one in the right version already installed. Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant{}pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Thu Dec 14 23:06:01 2006 From: "Mark Zottola mzottola*_*gmail.com" To: CCL Subject: CCL: Intramolecular Hydrogen Bonds: AIM vs GIAO NMR Message-Id: <-33259-061214221619-5744-9ZBvrVZTzxE/BeRoZ6Ga8Q[*]server.ccl.net> X-Original-From: "Mark Zottola" Content-Type: multipart/alternative; boundary="----=_Part_122166_15410127.1166152573153" Date: Thu, 14 Dec 2006 22:16:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Mark Zottola" [mzottola++gmail.com] ------=_Part_122166_15410127.1166152573153 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline A hydrogen bond is a bond. Therefore, location of a bond critical point is necessary to call a close contact a hydrogen bond. Corroborating evidence such IR or NMR shifts is simply that - corroboration. A shift in the value of some physical observable means there is an interaction. The exact nature of that interaction is unknown. To call that interaction something as specific as a hydrogen bond requires evidence that there is a bond. Hope this helps, Mark On 12/14/06, Sidney R. Santana santanasidney]*[yahoo.com.br < owner-chemistry,+,ccl.net> wrote: > > Sent to CCL by: "Sidney R. Santana" [santanasidney*yahoo.com.br] > Dear CCL Users, > > I am studying a system with a intramoleculecular hydrogen > > bonds assigned by AIM. But, It is possible to attain the > > same, or similar, assignment with GIAO NMR calculations by a shielding > > and deshielding analysis. > > Please, I would appreciate to read some > > point views about it. > > Best Regards, > > Sidney R. Santana > santanasidney_at_yahoo.com.br> > > > ------=_Part_122166_15410127.1166152573153 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
A hydrogen bond is a bond.  Therefore, location of a bond critical point is necessary to call a close contact a hydrogen bond.  Corroborating evidence such IR or NMR shifts is simply that - corroboration.  A shift in the value of some physical observable means there is an interaction.  The exact nature of that interaction is unknown.  To call that interaction something as specific as a hydrogen bond requires evidence that there is a bond. 
 
Hope this helps,
 
 
Mark

 
On 12/14/06, Sidney R. Santana santanasidney]*[yahoo.com.br <owner-chemistry,+,ccl.net > wrote:
Sent to CCL by: "Sidney R. Santana" [santanasidney*yahoo.com.br ]
Dear CCL Users,

I am studying a system with a intramoleculecular hydrogen

bonds assigned by AIM. But, It is possible to attain the

same, or similar, assignment with GIAO NMR calculations by a shielding

and deshielding analysis.

Please, I would appreciate to read some

point views about it.

Best Regards,

Sidney R. Santana
santanasidney_at_yahoo.com.br



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