From chemistry-request@server.ccl.net Mon Feb 4 04:55:41 2002 Received: from ibms.sinica.edu.tw ([140.109.40.252]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g149t9c04527 for ; Mon, 4 Feb 2002 04:55:40 -0500 Received: from localhost (syn@localhost) by ibms.sinica.edu.tw (8.10.2+Sun/8.10.2) with ESMTP id g149sro01155 for ; Mon, 4 Feb 2002 17:54:58 +0800 (CST) Date: Mon, 4 Feb 2002 17:54:53 +0800 (CST) From: Sergey Noskov To: chemistry@ccl.net Subject: CHARMM problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I had one , but very big problem. I would like to add another potential function to CHARMM instead traditional 6-12 for LJ. Based on our evaluation we would like to change function to Morse exponential potential for ion(single)-water interation. For water we would like to conserve TIP3 employed in CHARMM. Is it possible? If so, do we need to worry about cut-offs or not? I will be very gratefull to anybody who faced up with similar problem and found the way to solve it. With best regards, Sergey Sergey Noskov,Ph.D Institute of BioMedical Sciences Academia Sinica Taipei 11529,Taiwan R.O.C. tel:886-2-27899043 (work) 886-2-26600736 (home) fax:886-2-27887641 e-mail:syn@ibms.sinica.edu.tw From chemistry-request@server.ccl.net Mon Feb 4 08:22:04 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g14DM4c07782 for ; Mon, 4 Feb 2002 08:22:04 -0500 Received: from oncoirmb ([10.10.100.12]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-57574U3000L300S0V35) with SMTP id ca for ; Mon, 4 Feb 2002 09:21:49 -0400 Message-ID: <009e01c1ad7f$27df9320$0c640a0a@oncoirmb> From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) To: "CCL" Subject: Computer system requirements Date: Mon, 4 Feb 2002 09:23:37 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_009B_01C1AD5D.A04F4D40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_009B_01C1AD5D.A04F4D40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I am trying to set up a computer system for doing molecular modelling = (proteins, DNA) and computer simulations (Fortran and C++) on a very = limited budget. I think that I need either SGI (second hand is fine) or = PC Linux but I am not sure which one would be the better value for the = money (there would be just one user).=20 So any advice would be greatly appreciated and particularly: what are = the lowest requirements for SGI doing molecular modelling, in your = opinion which model is the best value, is it better to go with new PC = with LINUX or old SGI, where is the good place to purchase second hand = SGI or ideally does anyone here have an old but good SGI that you'd like = to get rid of/sell. I apologise for this (a little bit) out of contest question but I am = sure that you are the best group of people to ask this:-) Thanks for the ongoing help, Mira P.S. I will summarise answers (if any). _______________________________ Miroslava Cuperlovic-Culf Ph.D. Institute for Biomedical Research, 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 ------=_NextPart_000_009B_01C1AD5D.A04F4D40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All,

I am trying to set up a computer system = for doing=20 molecular modelling (proteins, DNA) and computer simulations (Fortran = and C++)=20 on a very limited budget. I think that I need either SGI (second = hand is=20 fine) or PC Linux but I am not sure which one would be the better value = for the=20 money (there would be just one user).

So any advice would be greatly = appreciated and=20 particularly: what are the lowest requirements for SGI doing molecular=20 modelling, in your opinion which model is the best value, is it = better to=20 go with new PC with LINUX or old SGI, where is the good place to = purchase second=20 hand SGI or ideally does anyone here have an old but good SGI that you'd = like to=20 get rid of/sell.

I apologise for this (a little bit) out = of contest=20 question but I am sure that you are the best group of people to ask=20 this:-)

Thanks for the ongoing = help,

Mira

P.S. I will summarise answers (if=20 any).

_______________________________
Miroslava=20 Cuperlovic-Culf Ph.D.
Institute for Biomedical Research,
37 = Providence=20 Street
Moncton, NB E1C 8X3
Canada
fax: = 506-862-4222
tel: =20 506-862-4848

------=_NextPart_000_009B_01C1AD5D.A04F4D40-- From chemistry-request@server.ccl.net Mon Feb 4 05:39:15 2002 Received: from mail.kemi.dtu.dk ([130.225.67.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g14AdFc05179 for ; Mon, 4 Feb 2002 05:39:15 -0500 Received: from [192.38.70.75] (pon.ok.dtu.dk [192.38.70.75]) by mail.kemi.dtu.dk (8.11.6/8.11.4) with ESMTP id g14Ad6H27642 for ; Mon, 4 Feb 2002 11:39:06 +0100 Mime-Version: 1.0 X-Sender: pon@mail.kemi.dtu.dk Message-Id: Date: Mon, 4 Feb 2002 11:39:27 +0100 To: CHEMISTRY@ccl.net From: Per-Ola Norrby Subject: High level for TMs Content-Type: text/plain; charset="us-ascii" ; format="flowed" Dear CCLers, I'd like to get some opinions on high level calculations on first row transition metal complexes, in particular for complexes with near-degenerate states. Furthermore, I'm interested in complexes used for homogeneous catalysis, so even very smal models frequently have 10-20 heavy atoms and as many hydrogens in addition to the metal. I've used various types of DFT, both pure and hybrid, for these types of systems for several years now. However, I've seen several indications recently that the relative energies of different spin surfaces can be wrong by up to 100 kJ/mol. This is, of course, unacceptable. I very much like the pragmatic fix proposed by Reiher et al, Theor. Chem. Acc. 107 (2001) 48-55, where they reparameterize the amount of exact exchange in B3LYP for organometallic complexes. However, having been burned once, I don't want to assume that one fixed parameterization is going to be valid for all first row transition metals. Thus, to apply this approach I need very good reference data for some experimentally inaccessible complexes. I'll have to obtain them computationally, but what level to use? Alternatively, I may not go for the modified DFT, but then I still need a theoretical level I can access, which will give me good relative energies (and the geometries, but maybe DFT can do this..?). So, what level can we trust for this? CCSD(T) has been proposed, but it's expensive, and we all know that it requires a large basis set, certainly much better than the double-zeta valence that is often used. And it is still only a perturbation method, so if the underlying HF is way off, no amount of perrturbation will fix it. However, I'd like to try it out if I can find a program that is reasonably efficient. I've heard rumors of linear scaling CCSD(T) or equivalent methods, does anyone know of an available implementation that will allow a calculation with ca 500 basis functions? How about MC methods? I'm trying out CASPT2, but what else is there? BTW, don't suggest any MP-method (MP2, LMP2,...). I've tried them for a couple of test cases, and the errors are much larger than with DFT. As a side issue, any suggestions of what type of experimental data to compare to? There are a couple of cases where population distributions among near-degenerate states can be measured, but this is not general enough, I also want to be able to predict cases where the energy difference is large. All the best Per-Ola -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@server.ccl.net Mon Feb 4 03:14:38 2002 Received: from gate3.oss.akzonobel.nl ([192.87.3.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g148Ebc02159 for ; Mon, 4 Feb 2002 03:14:37 -0500 Received: (from fwmaster@localhost) by gate3.oss.akzonobel.nl (8.9.1a/8.6.12) id JAA26914 for ; Mon, 4 Feb 2002 09:14:22 +0100 (MET) Received: by gate3.oss.akzonobel.nl via smap (V1.3) id sma025848; Mon, 4 Feb 02 09:13:22 +0100 Received: by triton.oss.intra with Internet Mail Service (5.5.2653.19) id <1CV3YHKF>; Mon, 4 Feb 2002 09:13:23 +0100 Message-ID: From: "Wagener, M. (Markus)" To: "'CHEMISTRY@ccl.net'" Subject: Extension of deadline for submittal of abstracts for the 6th ICCS Date: Mon, 4 Feb 2002 09:13:09 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" The following message has been sent to several relevant listservers, please excuse any duplication. The Organizing Committee of the Sixth International Conference on Chemical Structures to be held on June 2 - 6, 2002, in Noordwijkjerhout, The Netherlands, has decided to extend the deadline for the submittal of abstracts for oral and poster presentations to February 15, 2002. The extension will give scientists who might have missed the original deadline another chance to participate in this important triannual conference. For details about the conference and electronic submittal of abstracts please check the conference's website at http://www.chemweb.com/docs/6iccs/6iccs.html Markus Wagener on behalf of Guenter Grethe Chair, 6th ICCS -- ----------------------------------------------------------- Dr. Markus Wagener NV Organon MDI-CMC RK2330 phone: +31-412-661380 P.O. Box 20 FAX: +31-412-662539 5340 BH Oss Email: markus.wagener@organon.com The Netherlands ----------------------------------------------------------- -------------------------------------------------------------------- This message, including attached files, may contain confidential information and is intended only for the use by the individual and/or the entity to which it is addressed. Any unauthorized use, dissemination of, or copying of the information contained herein is not allowed and may lead to irreparable harm and damage for which you may be held liable. If you receive this message in error or if it is intended for someone else please notify the sender by returning this e-mail immediately and delete the message. -------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Feb 4 10:22:59 2002 Received: from uhura.curagen.com ([12.40.255.155]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g14FMxc10939 for ; Mon, 4 Feb 2002 10:22:59 -0500 Received: by mli8b5065ffbrad.curagen.com with Internet Mail Service (5.5.2653.19) id <1C7KACLL>; Mon, 4 Feb 2002 10:24:58 -0500 Message-ID: <715118539AC7D311A0DF009027DE6E190524AB1E@mli8b5065ffbrad.curagen.com> From: "Gusev, Vladimir" To: CCL Cc: "'pc@protoncomputers.com'" Subject: Summary: Fastest Intel/Amd Double Processor machine for MD Date: Mon, 4 Feb 2002 10:24:54 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Initial question: > Hello, > I am seeking information about assembling/buying a complete linux Intel or > AMD-based system (double processor) that would be fastest at current > standards (for Intel, I guess 2.2 GHz, 0.13 micron processor is mandatory). > Please let me know about available options - complete systems, parts, > overclocking experiences etc, as well as benchmarks. This is to run an MD > codes such as for example Gromacs to model protein confirmations.The replies > will be summarized. Thank you. > > Vladimir Replies: ======== It looks like a double Athlon MP system is faster than Pentium 4 for raw calculations. Pentium 4 is still faster for multimedia, but I think that does not concern you. The hard disk data transfer rate is a problem. I am building a system like that with a FastTrak100 TX4 quad IDE controller and four ATA100 20 GB drives. In several reviews I saw rates close to the limit of the 66 MHz PCI bus. I am also going to use the ASUS A7M266-D motherboard which allows for use of up to 2GB of unbuffered memory. Iam going to use the "True CAS2" (2-2-2) memory rather than standard CAS2 (2-3-3) RAM. The other two motherboards on the market, Tyan S2466 and MSI MS-6510 require registered memory. Slawomir Janicki slawek@attbi.com ======= 1.I had fabulous luck with Proton Computers located on the internet. 2.No they were not toys. I wanted to run Open BSD on two three homed host firewalls for a secure VPN encoded with Blowfish. They took the time to talk to me a lot about what I needed and then did a superb custom job at a reasonable price. Write the guy on email. Talk to him. If you don't like it, try somebody else. Good luck, CB Carla (carlabrg@discover-net.net) ======= From: Proton Computers [mailto:pc@protoncomputers.com] > Sent: Wednesday, January 30, 2002 11:27 PM > To: Gusev, Vladimir > Subject: Re: Fastest Intel/Amd Double Processor machine for MD > > Hi, > > Here's an example system that I could put together for you. > > -Asus A7M266D Motherboard > - (2) AthlonXP 2000+ > -512mb Registered ECC DDR Memory > -Maxtor 60gig ATA133/7200rpm HD > -Gainward Geforce2 MX 32mb AGP Card > -Intel Pro 100S NIC > -Sony 52X CDROM > -Sony Floppy Drive > -Inwin Q500 Full Tower > -Enermax 450w PSU > > $1675.00 > > The price includes my unlocking the CPU's, finding the highest stable > overclocked speed, and testing for 24hrs. (at least). I included $50.00 in > the budget for CPU Coolers, but would probably test a few different units > out on the system, let you know the results, then you could decide what you > wanted to go with. > > Anyway, if you want a smaller case, a more powerful PSU, a larger hard > drive, exhaust and intake fans put on the sides and top of the case, etc. > It's no problem. > > Thanks, Ned > > Proton Computers > > Phone: 847-295-1645 > Web: http://protoncomputers.com > LEGAL NOTICE - Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this e-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. From chemistry-request@server.ccl.net Mon Feb 4 12:03:18 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g14H3Hc13011 for ; Mon, 4 Feb 2002 12:03:17 -0500 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g14I9xH25673 for chemistry@ccl.net; Mon, 4 Feb 2002 10:09:59 -0800 Received: from JNAUSS-PC.accelrys.com (jnauss-pc.sd.accelrys.com [172.30.26.50]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g14I9x925664 for ; Mon, 4 Feb 2002 10:09:59 -0800 Message-Id: <5.1.0.14.0.20020204090052.01f82048@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 04 Feb 2002 09:02:23 -0800 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training with InsightII in Italy Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys Inc. will be holding a pair of 2-day workshops at CICAIA, Universita` di Modena e Reggio Emilia, Modena, Italy. On 9-10 April, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On 11-12 April, the "CHARMm Workshop" will be offered. This course provides an overview of the simulations engine CHARMm used for molecular mechanics and molecular dynamics calculations on biological systems. The course is designed to take the student through the basics of CHARMm, understanding the data flow and command language, and providing some practical examples. Force fields used in CHARMm will also be discussed. Attendees should possess knowledge of basic UNIX commands and a basic understanding of molecular modeling. Some experience with InsightII is recommended. Fees for each 2-day course are EUR1120 commercial, EUR560 government, and EUR450 academic. However, register for both courses and receive a 25% discount for the second course. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey Nauss +1-858-799-5555 Andrew English +1-781-359-1260 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Manager, US Training Fax: (858) 799-5100 Accelrys Inc. E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/ San Diego, CA 92121-3752 From chemistry-request@server.ccl.net Mon Feb 4 14:58:06 2002 Received: from mail.laposte.net ([160.92.113.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g14Jw6c16159 for ; Mon, 4 Feb 2002 14:58:06 -0500 Received: from nouveaupc (80.13.205.170) by mail.laposte.net (5.5.044) id 3C4BFED4000F1D1F for CHEMISTRY@ccl.net; Mon, 4 Feb 2002 20:57:51 +0100 Message-ID: <00ab01c1adb5$8b400900$0b00000a@nouveaupc> From: "Alexandre Hocquet" To: Subject: AIM quality of the electronic density Date: Mon, 4 Feb 2002 20:52:53 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear CCLers, It is common procedure to make a single point calculation at a higher level of theory/basis set in order to get a more reliable energy, even though the geometry of the molecule is not exactly at a minimum for this higher level of theory. I wonder if it is also true if one is interested in the electronic density. In other words, would a AIM analysis, for example, be more reliable on a density calculated at a true minimum, with all forces vanishing, but with a lower level of theory or for a higher level of theory , but for an density corresponding to a bad geometry ? Thanks in advance for your commentaries, ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomol�culaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------