From chemistry-request@ccl.net Wed Jun 8 02:29:59 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.194]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j586Tu58009900 for ; Wed, 8 Jun 2005 02:29:56 -0400 Received: by wproxy.gmail.com with SMTP id 58so163212wri for ; Tue, 07 Jun 2005 23:29:56 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=A3UguDY2r3vQEVgZyHiWzgE9SRzDTwbhUVitkUfqtcMSjTr2JmfqjtHkZcNRcVkFQr4ZKVEiaShV/4QSEwctGCUMu/4DDYEA2ehutbLHJoCxficvdGAc3ySlS7umW1grm0DXIC4A8CcR2tKvXvPdBRC8Ef9jTvm7GLqXzxuEahU= Received: by 10.54.97.19 with SMTP id u19mr3070645wrb; Tue, 07 Jun 2005 22:29:55 -0700 (PDT) Received: by 10.54.21.13 with HTTP; Tue, 7 Jun 2005 22:29:55 -0700 (PDT) Message-ID: <270bc69d0506072229732ab339.-at-.mail.gmail.com> Date: Tue, 7 Jun 2005 23:29:55 -0600 From: Jaremy Creechley Reply-To: Jaremy Creechley To: chemistry.-at-.ccl.net Subject: Gaussian / Debian Error Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j586Tx58009911 Hello, Has anyone had any problems recently with Gaussian 2003 running on Debian (Sarge)? We had g03 compiled and running fine for many months, but when I tried to run it recently it returns this error: g03: relocation error: /work/pgi/linux86/5.2/lib/libpthread.so.0: symbol _errno, version GLIBC_2.0 not defined in file libc.so.6 with link time reference We have tried to reinstall Debian and recompiling g03 several times. PGroup said that its an error with some RHEL users, but a libc6-compat library fixed it, but otherwise they don't know about it. Debian ran well, I don't know if the new sarge->stable transition changed anything. Would anyone suggest PGI 6.0 as necessary? Thanks, ~ Jaremy Creechley Student of Physics, University of Wyoming creechley.-at-.gmail.com 208.484.7555 From chemistry-request@ccl.net Wed Jun 8 01:53:19 2005 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j585rFfS007719 for ; Wed, 8 Jun 2005 01:53:16 -0400 Received: from laurence.mbi.ucla.edu (d-128-97-138-48.chem.ucla.edu [128.97.138.48]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id j585r6Kg004126; Tue, 7 Jun 2005 22:53:12 -0700 Message-Id: <6.1.2.0.2.20050607214538.038ad430.-at-.po.chem.ucla.edu> X-Sender: lavelle.-at-.po.chem.ucla.edu X-Mailer: QUALCOMM Windows Eudora Version 6.1.2.0 Date: Tue, 07 Jun 2005 22:52:00 -0700 To: amber.-at-.scripps.edu, chemistry.-at-.ccl.net From: Laurence Lavelle Subject: Protein dynamics. Cc: "David A. Case" , Konrad Hinsen Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Both David and Konrad had several useful and thoughtful comments some of which are given below. I am still thinking about them. To a first approximation David is saying we need faster computers, while Konrad is saying we need more experiments. Even a small 100 residue protein (approx 1700 atoms) needs approximately 6000 waters (18000 atoms) to appropriately solvate (periodic box, with minimal switched cutoffs so as to avoid protein-protein interactions) the protein in an all atom Amber MD simulation for 100+ ps ... The TIP3P water model was equilibrated at 300 K and 1 atm. In the literature I see it used at temperatures below and above 300 K. In fact it is used in non-isothermal simulations. Is the TIP3P water model ok to use for (isothermal) MD at 400 K and 1 atm ? Also various numbers are used as the minimum distance between solvent and protein atoms (when adding water). I use 2.3 A. With respect to Konrad's comments. I had thought the frictional co-efficient was a constant in LD and it was chosen based on the water-protein interface. In interesting that it is (possibly) the intra-protein contacts that dominate. Although I would think this would scale with the size of the protein and therefore the frictional co-efficient would be protein dependent (or at least have two terms taking into account the water-protein and protein-protein contacts and these in turn would change during a simulation as the protein conformation changed increasing or decreasing the solvent accessible protein surface). I think the key point here ("For slow large-scale motions, you can leave out electrostatics completely, assuming no unfolding of course ...") is what is considered a structural change vs unfolding. Thanks again for your thoughtful comments. Laurence >On Mon, Jun 06, 2005, Laurence Lavelle wrote: > > > By protein motion I mean a folded protein in a constant temperature > > simulation (for example with a distance dependent dielectric, no > > electrostatic cutoffs, no periodic boundaries) and comparing the protein > > dynamics at different temperatures. > >With the above conditions (no solvent, distance dependent dielectric) there is >little reason to expect that either the average structure or the dynamics you >see in the simulation will be realistic. If you want to get any reasonable >account of protein dynamics, you need to be looking at MD simulations in >explicit solvent. If you want good results as a function of temperature, you >should take care that the water model you are using is known to produce good >dynamical results vs. temperature for pure water. > >...dac >On 06.06.2005, at 23:43, Laurence Lavelle wrote: > >>In looking at the dynamical motion of a protein, is Amber (Cornell et >>al. (1994) force field) (Amber 99 parameters) considered a reasonably >>realistic protein force field (or, as good as or better than most) ? >> >>In looking at the dynamical motion of a protein (for example using >>Amber), what are the pros and cons to doing Molecular Dynamics vs >>Langevin Dynamics vs Monte Carlo ? > >It all depends on what dynamical quantities you wish to calculate, and >on which time scales. > >If you look at long time scales for a protein that has a single stable >conformation, then you can get good results with very much simpler >models at much lower cost. See > > K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, G.R. >Kneller > Harmonicity in slow protein dynamics > Chem. Phys. 261, 25-37 (2000) > >for an example. At the other end of the time scale spectrum, if your >study involves quantum effects, no Molecular Mechanics model will be >good enough. > >As for sampling techniques, note that Monte Carlo is not a dynamical >technique at all (it has no time scale), even though in some situations >a time scale can be assigned a posteriori. Langevin and Brownian >dynamics add an implicit source of friction and thermal energy, which >should correspond to some physical feature of the model, i.e. the >explicit modelling should be less detailed. > >In this context, it is worth pointing that the major source of friction >in a protein is not the solvent, as is frequently believed, but fast >interactions in the protein itself. See the article quoted above for a >demonstration. > >>{Some will say it depends on the details (distance dependent >>dielectric vs explicit solvent water molecules, no cutoffs vs with >>switched or shifted cutoffs, with or without periodic boundary >>conditions, etc.). However I am > >Again this depends on the time scales. For slow large-scale motions, >you can leave out electrostatics completely, assuming no unfolding of >course, because on such a coarse length scale the charge density is >practically zero. On the other hand, for localized events, a correct >representation of electrostatics is very important. > >> hoping (in addition to the above two questions) to get a general >>sense of how realistic MD, LD and MC are with respect to illustrating >>protein motion. > >We don't know that much about how realistic simulations of protein >dynamics are. Experimental information is mostly on very small time >scales or on time scales so long that they are out of reach of >simulations. In between those two extremes, there is nothing that >simulations could be tested against. > >Konrad Hinsen From chemistry-request@ccl.net Wed Jun 8 07:44:32 2005 Received: from cuces2.unisi.it (cuces2.unisi.it [193.205.4.8]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58BiTxv025851 for ; Wed, 8 Jun 2005 07:44:29 -0400 Received: from PMAS-DAEMON.mailsrv.unisi.it by mailsrv.unisi.it (PMDF V6.2-X17 #30967) id <01LP7WLZXNCW8ZDZ8U[at]mailsrv.unisi.it> for chemistry[at]ccl.net; Wed, 08 Jun 2005 13:00:15 +0200 (MET-DST) Received: from CONVERSION-DAEMON.mailsrv.unisi.it by mailsrv.unisi.it (PMDF V6.2-X17 #30893) id <01LP7WLN26SG90MTR5[at]mailsrv.unisi.it>; Wed, 08 Jun 2005 12:59:58 +0200 (MET-DST) Received: from unisi.it (pc-manetti.smin.unisi.it [172.16.53.250]) by mailsrv.unisi.it (PMDF V6.2-X17 #30967) with ESMTPA id <01LP7WLMXUZY8ZE2S0[at]mailsrv.unisi.it>; Wed, 08 Jun 2005 12:59:58 +0200 (MET-DST) Date: Wed, 08 Jun 2005 13:00:30 +0200 From: Fabrizio Manetti Subject: problems with NAMD To: CCL Cc: namd[at]ks.uiuc.edu Message-id: <42A6CFCE.9010004[at]unisi.it> MIME-version: 1.0 Content-type: multipart/alternative; boundary="Boundary_(ID_arCM6YlZvAABOBBKyWGdnA)" X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-PMAS-Software: PreciseMail V2.1-1 [050607] (mailsrv.unisi.it) X-PMAS-Final-Score: 0.600 X-PMAS-Spam-Level: X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO,HTML_MESSAGE, HTML_TITLE_EMPTY autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. --Boundary_(ID_arCM6YlZvAABOBBKyWGdnA) Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 8BIT Dear CCLers, I have several questions for you on the use of NAMD software. I apply the following protocol to a protein structure: 1) minimization of a pdb protein (explicit solvation, water), 2) MD simulation, 3) minimization (explicit solvation, water) of some frames from MD. However, I didn't find in the literature any example where NAMD has been used for minimization purposes after a MD simulation. Do you think such a protocol is correct? Moreover, when I minimize frames from MD, I always observe a problem with hydrogens bound to the indolic nitrogen of TRP residues: this hydrogen is never coplanar with respect to the whole indole cycle. I tried more than once, modifying different parameters, but I always got the same problem. Do you have any suggestion to solve such a problem? Thank you very much for your collaboration. Regards, Fabrizio ps : A similar email was sent about one month ago to the NAMD support, but I did not receive any answer, yet. -- Dr. Fabrizio Manetti Dept. Farmaco Chimico Tecnologico Universit` degli Studi di Siena Via Aldo Moro 53100 Siena, Italy Tel: +39 0577 234330 Fax: + 39 0577 234333 Email:manettif[at]unisi.it --Boundary_(ID_arCM6YlZvAABOBBKyWGdnA) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT Dear CCLers,
I have several questions for you on the use of NAMD software.

I apply the following protocol to a protein structure:
1) minimization of a pdb protein (explicit solvation, water),
2) MD simulation,
3) minimization (explicit solvation, water) of some frames from MD.

However, I didn't find in the literature any example where NAMD has been used for minimization purposes after a MD simulation.
Do you think such a protocol is correct?

Moreover, when I minimize frames from MD, I always observe a problem with hydrogens bound to the indolic nitrogen of TRP residues: this hydrogen is never coplanar with respect to the whole indole cycle.
I tried more than once, modifying different parameters, but I always got the same problem. Do you have any suggestion to solve such a problem?

Thank you very much for your collaboration.

Regards,
Fabrizio


ps : A similar email was sent about one month ago to the NAMD support, but I did not receive any answer, yet.
--
Dr
          Dr. Fabrizio Manetti
Dept. Farmaco Chimico Tecnologico
    Università degli Studi di Siena
                  Via Aldo Moro
               53100 Siena, Italy
           Tel: +39 0577 234330
          Fax: + 39 0577 234333
--Boundary_(ID_arCM6YlZvAABOBBKyWGdnA)-- From chemistry-request@ccl.net Wed Jun 8 04:18:09 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j588I8s3016094 for ; Wed, 8 Jun 2005 04:18:08 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j588I8SC016093 for chemistry[at]ccl.net; Wed, 8 Jun 2005 04:18:08 -0400 Date: Wed, 8 Jun 2005 04:18:08 -0400 Message-Id: <200506080818.j588I8SC016093[at]server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request[at]ccl.net using -f From: "Zhenyu, , Yang" To: chemistry[at]ccl.net X-Web-Message-Number: 050608041625-15956 Subject: W:helpproblem on Gamess/Tinker for QM/MM calculation X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I am doing some QM/MM calculations by Gamess/Tinker, I plan to build a water box in my system which will be treated as MM atoms. But I don't know how to set the boundary condition for the water box in Gamess input? Anybody could enlighten me on this problem?? Thanks in advance. Best Regards Yang Zhenyu State Key Laboratory of Nonlinear Mechanics (LNM) Institute of Mechanics, Chinese Academy of Sciences No.15 Beisihuanxi Road Beijing 100080, P. R. China yangzy[at]lnm.imech.ac.cn From chemistry-request@ccl.net Wed Jun 8 06:26:43 2005 Received: from relay.unizar.es (ortiz.unizar.es [155.210.11.72]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58AQeFW022526 for ; Wed, 8 Jun 2005 06:26:41 -0400 Received: from [155.210.92.49] (neptuno.unizar.es [155.210.92.49]) (authenticated bits=0) by relay.unizar.es (8.13.4/8.12.3) with ESMTP id j58AQOXL029783; Wed, 8 Jun 2005 12:26:27 +0200 Message-ID: <42A6C7D7.70107~at~unizar.es> Date: Wed, 08 Jun 2005 12:26:31 +0200 From: Pablo Echenique Robba Reply-To: pnique~at~unizar.es User-Agent: Mozilla Thunderbird 1.0 (X11/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: dinamica~at~webcable.com.br, CCL list CC: Jose Luis Alonso Subject: Re: CCL:existence of HF-SCF solutions References: <42A5CD4E.4000006~at~unizar.es> <20050608101505.GA13205~at~biomim09.iq.usp.br> In-Reply-To: <20050608101505.GA13205~at~biomim09.iq.usp.br> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Mail-Scanned: Criba 2.0 + Clamd en Unizar X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Guilherme, Thank you very much for your precise and useful answer. I have one more question however: when you answer to my point b), you don't mention anything about checking that the minimum is not only local but also global. Are there checks for this? Thanks and regards, Pablo. Guilherme Menegon Arantes wrote: >On Tue, Jun 07, 2005 at 06:37:34PM +0200, Pablo Echenique Robba wrote: > > >>Hello everybody. >> >>What I wanted to know is whether someone could indicate to me where may >>I find a discussion on the existence of solutions of the HF-SCF >>iterative procedure. I first enumerate briefly what I know: >> >>1) The HF equations HAVE solutions (Lieb and Simon, 1977). >>2) Any solution of the HF equations is an extremal, with no indication >>about its being a maximum, a saddle point or a minimum whatsoever. >>3) The SCF method DOES NOT always converge. Of course, when it does >>converge, the wave function that results is indeed a solution of the HF >>equations. Again, with no indication about its being a maximum, a saddle >>point or a minimum. >> >>My two questions are related to point 3: >> >>a) When does the SCF converge? >>b) How do we know, if it converged, that it did it to a minimum (and not >>to a maximum or to a saddle point)? >> >>I would thank very much any hint to articles or books discussing this. I >>mean, further than the typical "we hope it converge because our basis >>sets and our starting point are so good". >> >> > > >Hi Pablo, > >I see two issues here. One is the analicity of the HF equations. And >they do have solutions. The other issue is the computational or >numerical procedure used to find those solutions. > >Regarding b), we know that the converged solution is a minimum by >calculating the second derivative of the solution wrt the (MO) >coeficients, this is the "stability" check found in some computer >programs. > >Regarding a), there are many different SCF algorithms. Some first order >(use only 1st derivatives wrt to coeficients), other second order (use >1st and 2nd derivatives) and quasi-second order (use some approximation >to the 2nd derivatives). Each type has diffrent convergence properties, >and pratical/observed convergence depends on the region of the >coeficient space which you start your optimization. > >There are many reviews on these subjects, try: >author = "T. Helgaker", >title = "Optimization of Minima and saddle points", >booktitle = "Lectures Notes in Quantum Chemistry - European Summer >School in Quantum Chemistry", >editor = "B. O. Roos", >year = 1992, >volume = 1, >publisher = "Springer-Verlag", >pages = {295-324}, >address = "Berlin", > >or > >author = "H. B. Schlegel", >title = "Optimization of equilibrium geometries and transition >structures", >journal = "Adv. Chem. Phys." , >year = 1987, >volume = 67, >pages = {249-286}, > >Hope it helps, > >Guilherme > > > > -- ------------------------------------ Pablo Echenique Robba Departamento de Fisica Teorica & Instituto de Biocomputacion y Fisica de los Sistemas Complejos BIFI Universidad de Zaragoza 50009 Zaragoza Spain Tel.: 34 976761260 E-mail: pnique~at~unizar.es ------------------------------------ From chemistry-request@ccl.net Wed Jun 8 06:15:34 2005 Received: from gvedoh01.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58AFW6X021890 for ; Wed, 8 Jun 2005 06:15:33 -0400 To: CCL Subject: Re: CCL:a secure Xterm emulator MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy~at~givaudan.com Date: Wed, 8 Jun 2005 12:15:30 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 6.5.3|September 14, 2004) at 08/06/2005 12:15:33, Serialize complete at 08/06/2005 12:15:33 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j58AFY6X021900 Dear Colleagues, Thank you for the answers. I have ordered Reflection X, because that would be easiest to use for my organic chemist colleagues. Regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy~at~givaudan.com From chemistry-request@ccl.net Wed Jun 8 15:40:15 2005 Received: from albert.genomecenter.ucdavis.edu (albert.genomecenter.ucdavis.edu [128.120.136.148]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58JeD5t004521 for ; Wed, 8 Jun 2005 15:40:13 -0400 Received: from albert.genomecenter.ucdavis.edu (localhost.localdomain [127.0.0.1]) by albert.genomecenter.ucdavis.edu (8.12.8/8.12.8) with ESMTP id j58IeDeK004259 for ; Wed, 8 Jun 2005 11:40:13 -0700 Received: from localhost (duan@localhost) by albert.genomecenter.ucdavis.edu (8.12.8/8.12.8/Submit) with ESMTP id j58HO27h004200; Wed, 8 Jun 2005 10:24:02 -0700 Date: Wed, 8 Jun 2005 10:24:02 -0700 (PDT) From: Yong Duan To: amber|at|scripps.edu cc: chemistry|at|ccl.net Subject: Re: AMBER: Protein dynamics. In-Reply-To: <6.1.2.0.2.20050607214538.038ad430|at|po.chem.ucla.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net If you only need 100+ ps for a small system of 18,000 atoms, I can do it on my laptop for you free of charge. This should take no more than a day, if that is not too long for you. However, I will use PME instead. PME is the method of choice for highly ionic system. Tried others in those early "dark days". yong On Tue, 7 Jun 2005, Laurence Lavelle wrote: > Even a small 100 residue protein (approx 1700 atoms) needs approximately > 6000 waters (18000 atoms) to appropriately solvate (periodic box, with > minimal switched cutoffs so as to avoid protein-protein interactions) the > protein in an all atom Amber MD simulation for 100+ ps ... From korkin@nanoandgiga.com Wed Jun 08 17:06:15 2005 Message-ID: <1118264771.42a75dc3a1356 {} nanoandgiga.com> Date: Wed, 8 Jun 2005 16:06:11 -0500 From: Anatoli Korkin To: chemistry {} ccl.net Subject: MRS Fall Meeting/Boston: Combinatorial Methods & Informatics in Materials Science Dear CCL members, I would like to remind you about approaching deadline for abstracts submission abstracts for the MRS 2005 Fall symposium in Boston - June 21st. Those of you who plan to attend this meeting, we encourage you to submit your paper to our Symposoium on COMBINATORIAL METHODS AND INFORMATICS IN MATERIALS SCIENCE: http://www.mrs.org/meetings/fall2005/program/f05_cfp_ll.html Best Regards, Anatoli Korkin Nano & Giga Solutions 1683 E.Spur St Gilbert, AZ 85296 Tel/Fax: 480-539-4754 C-phone: 480-329-5710 E-mail: korkin {} nanoandgiga.com http://www.nanoandgiga.com From chemistry-request@ccl.net Wed Jun 8 17:26:03 2005 Received: from zproxy.gmail.com (zproxy.gmail.com [64.233.162.193]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58LPxFG009491 for ; Wed, 8 Jun 2005 17:25:59 -0400 Received: by zproxy.gmail.com with SMTP id 13so429799nzn for ; Wed, 08 Jun 2005 14:25:58 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=LYU76pIVWzOj0+lTYMHyaumCEcbPDML8W81UFT1nbOZIzgeMIqKpe3wD9UIHqlWBbNWrzTyJsKbHKg8HyOl0jqPtpsz7NAnfXdzz7eJVm7vhbAKcbJMHUWB+j9bdZPrrzJ9vYmAvvzqU58e8c70Jw3qzgG1zsORXWyx4zhCkM2k= Received: by 10.36.58.19 with SMTP id g19mr947730nza; Wed, 08 Jun 2005 14:25:58 -0700 (PDT) Received: by 10.36.7.4 with HTTP; Wed, 8 Jun 2005 14:25:58 -0700 (PDT) Message-ID: Date: Wed, 8 Jun 2005 17:25:58 -0400 From: Gustavo Seabra Reply-To: To: CCL Subject: Reflections about the list Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=1.4 required=5.0 tests=RCVD_BY_IP,REPLY_TO_EMPTY autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j58LQ3FG009504 Dear All, I just have a questio that I would appreciate to hear your opinions. I participate in other mailing lists, and what is common there is that, whenever you reply to a message, your reply automatically goes to the list, not to the personal e-mail of the original poster. The exceptions would be when he or she have defined a "reply to" address, in which case it also goes to that address. But, it **always** goes to the list as well. Here in CCL this doesn't happen, unless you are careful enough to select "reply all" instead of simply "reply". As a consequence, my mailbox gets filled with questions, and just a few answers. My personal opinion is in favor of the common way of the other lists, and the reason is that I have learned **a lot** from the answers to question posted by other people as well as to my questions. Sometimes I just like to follow a thread, even if I don't know any answer to it, and end up knowing more than before. That just doesn't happen naturally with CCL, unless it's a thread that people are being careful to send the reply to all (we do see this in some general interest issues), if we ask the poster for a summary or if he voluntarily posts a summary. Otherwise, only he learns from the answers. Would anybody know why the CCL behavior is different? Is there anybody else here who feels he could learn more by following other threads as well? Thanks, -- --------------------------------------------------------------------------------------------- Gustavo Seabra Postdoctoral Associate Quantum Theory Project University of Florida Registered Linux user number 381680 Say NO! to software patents: http://www.nosoftwarepatents.com --------------------------------------------------------------------------------------------- If at first you don't succeed... ...skydiving is not for you. From chemistry-request@ccl.net Wed Jun 8 17:20:31 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.195]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58LKTPh009209 for ; Wed, 8 Jun 2005 17:20:29 -0400 Received: by wproxy.gmail.com with SMTP id 58so530860wri for ; Wed, 08 Jun 2005 14:20:29 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=PpvxNsQhX/y+T9cWK4ffAbzFa1DECpe0Hgb4Ux4IYPI+3r6FLwXXRqUPd3hiuL6iyboiW2RwFjipBz6PPqXKtEj8G/U0eokOUcPRGfLHfQeGwaWKHbziu67FNdf5/XIjjeGPzncHsZUEMFrYg2iBK1hQ96if4KX4Ifb5xqf+htQ= Received: by 10.54.34.16 with SMTP id h16mr5026275wrh; Wed, 08 Jun 2005 14:20:29 -0700 (PDT) Received: by 10.54.21.13 with HTTP; Wed, 8 Jun 2005 14:20:29 -0700 (PDT) Message-ID: <270bc69d0506081420685a2614 #%# mail.gmail.com> Date: Wed, 8 Jun 2005 15:20:29 -0600 From: Jaremy Creechley Reply-To: Jaremy Creechley To: chemistry #%# ccl.net Subject: Gaussian / Debian Problem resolved Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j58LKVPh009213 I wrote yesterday about a relocation error in Debian. Fortunantely the problem has been solved. We had an older version of the PGI comiler installed, the 5.2-1 instead of the 5.2-4, which has solved the issue. Sarge seems stable with Gaussian 03. Thanks for the help, -- ~ Jaremy Creechley Student of Physics, University of Wyoming creechley #%# gmail.com From chemistry-request@ccl.net Wed Jun 8 18:26:57 2005 Received: from PVEXCH01.PV.PVPANTHER.NET (pvexch01.pv.pvpanther.net [129.207.7.21]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58MQpRi011621 for ; Wed, 8 Jun 2005 18:26:51 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C56C72.94FB7D4C" Subject: RE: a secure Xterm emulator Date: Wed, 8 Jun 2005 16:39:07 -0500 Message-ID: <1D58F94275E4274F8C83B7A880F2D3BE0873F4 _()_ PVEXCH01.PV.PVPANTHER.NET> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: a secure Xterm emulator Thread-Index: AcVsZp3W0wlv87VaQpWjRPVFDUorkAAC+HIN From: "Fan,Huajun" To: , "CCL" X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE,HTML_50_60, HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C56C72.94FB7D4C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Dr Borosy =20 May I ask how much ReflextX cost? I am also interested in buying one. =20 Thanks. =20 Huajun Fan Email: hjfan _()_ pvamu.edu Tel: (936) 857-2616 Prairie View A&M University Chemistry Department PO Box 4107 Prairie View, TX 77446-4107 =20 ________________________________ From: Computational Chemistry List on behalf of = andras.borosy _()_ givaudan.com Sent: Wed 6/8/2005 5:15 AM To: CCL Subject: CCL:a secure Xterm emulator Dear Colleagues, Thank you for the answers. I have ordered Reflection X, because that = would be easiest to use for my organic chemist colleagues. Regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy _()_ givaudan.com -=3D This is automatically added to each message by the mailing script = =3D- To send e-mail to subscribers of CCL put the string CCL: on your = Subject: line and send your message to: CHEMISTRY _()_ ccl.net Send your subscription/unsubscription requests to: = CHEMISTRY-REQUEST _()_ ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ------_=_NextPart_001_01C56C72.94FB7D4C Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =0A= =0A= =0A= =0A= =0A= =0A= CCL:a secure Xterm emulator=0A= =0A= =0A=
=0A=
Hi Dr = Borosy
=0A=
 
=0A=
May I ask how much ReflextX = cost? I am also =0A= interested in buying one.
=0A=
 
=0A=
Thanks.
=0A=
 
=0A=
=0A=
Huajun =0A= Fan
=0A=
Email: =0A= hjfan@pvamu.edu
=0A=
Tel: (936) = 857-2616
=0A=
=0A=
Prairie View A&M University
=0A=
Chemistry Department
=0A=
PO Box 4107
=0A=
Prairie View, TX 77446-4107
=0A=
 
=0A=

=0A=
=0A= From: Computational Chemistry List = on behalf of =0A= andras.borosy _()_ givaudan.com
Sent: Wed 6/8/2005 5:15 = AM
To: =0A= CCL
Subject: CCL:a secure Xterm emulator

=0A=
=0A=

Dear Colleagues,

Thank you for the answers. I = have =0A= ordered Reflection X, because that would
be easiest to use for my = organic =0A= chemist colleagues.

Regards,

Dr. Andras Borosy
Seniour =0A= Scientist
Delivery Systems, Fragrance Research
Givaudan Schweiz =0A= AG
Ueberlandstr. 138
8600 D|bendorf
Switzerland
tel: + =0A= 41-1-8242164
fax: +41-1-8242926
e-mail: =0A= andras.borosy _()_ givaudan.com



-=3D This is automatically = added to each =0A= message by the mailing script =3D-
To send e-mail to subscribers of = CCL put the =0A= string CCL: on your Subject: line
and send your message to:  =0A= CHEMISTRY _()_ ccl.net

Send your subscription/unsubscription requests = to: =0A= CHEMISTRY-REQUEST _()_ ccl.net
HOME Page: http://www.ccl.net   | Jobs = Page: http://www.ccl.net/jobs

If = your is =0A= mail bouncing from ccl.net domain due to spam filters, please
use the = Web =0A= based form from CCL Home =0A= Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+





=0A= =0A= =0A= ------_=_NextPart_001_01C56C72.94FB7D4C-- From chemistry-request@ccl.net Wed Jun 8 18:31:12 2005 Received: from osgood.cc.nd.edu (osgood.cc.nd.edu [129.74.250.227]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j58MV9eD011782; Wed, 8 Jun 2005 18:31:09 -0400 Received: from localhost (localhost [127.0.0.1]) by osgood.cc.nd.edu (Switch-3.1.7/Switch-3.1.7) with ESMTP id j58MV3x8004477; Wed, 8 Jun 2005 17:31:03 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Wed, 8 Jun 2005 17:31:03 -0500 Message-ID: <1118269863.42a771a79c4c4[at]webmail.nd.edu> Date: Wed, 8 Jun 2005 17:31:03 -0500 From: Jan K Labanowski To: Gustavo Seabra Cc: CCL Subject: Re: CCL:Reflections about the list References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Wed, 08 Jun 2005 17:31:09 -0500 (EST) X-ND-Virus-Scan: engine v4.4.00; dat v4509 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Gustavo, I added the Reply-To: chemistry[at]ccl.net header to CCL messages. As to reasons... The idea was that once people get a bunch of answers they will post a "summary" to CCL (please do!!!). This would limit the traffic on the list. With the amount of spam that we get every day, people are trying to limit the amount of email they receive. What usually happens is that we unsubscribe from the busy lists that we CAN CONTROL and still receive tons of spam that we cannot control. Moreover, we are all swamped with "memos" at our institutions that we cannot control either. This has the unfortunate effect that many of us slowly end our participation in the lists since we are overwhelmed with the amount of mail and spam. As a result, however, we end up with the pure spam in our mailboxes. We will see in a few days how the default "reply to CCL" works. If subscribers start yelling at me, I will just restore the old default, i.e, replies by default will go to the original author. Jan -- Jan K. Labanowski, Ph.D. Tel. (574) 631-5465 Science Computing Facility FAX (574) 631-9293 University of Notre Dame 225 Nieuwland Science Hall Notre Dame, IN 46556-5670 Quoting Gustavo Seabra : > Dear All, > > I just have a questio that I would appreciate to hear your opinions. > > I participate in other mailing lists, and what is common there is > that, whenever you reply to a message, your reply automatically goes > to the list, not to the personal e-mail of the original poster. The > exceptions would be when he or she have defined a "reply to" address, > in which case it also goes to that address. But, it **always** goes > to the list as well. > > Here in CCL this doesn't happen, unless you are careful enough to > select "reply all" instead of simply "reply". As a consequence, my > mailbox gets filled with questions, and just a few answers. > > My personal opinion is in favor of the common way of the other lists, > and the reason is that I have learned **a lot** from the answers to > question posted by other people as well as to my questions. Sometimes > I just like to follow a thread, even if I don't know any answer to it, > and end up knowing more than before. That just doesn't happen > naturally with CCL, unless it's a thread that people are being careful > to send the reply to all (we do see this in some general interest > issues), if we ask the poster for a summary or if he voluntarily posts > a summary. Otherwise, only he learns from the answers. > > Would anybody know why the CCL behavior is different? Is there anybody > else here who feels he could learn more by following other threads as > well? > > Thanks, > > -- > --------------------------------------------------------------------------------------------- > Gustavo Seabra Postdoctoral Associate > Quantum Theory Project University of Florida > Registered Linux user number 381680 > Say NO! to software patents: http://www.nosoftwarepatents.com > --------------------------------------------------------------------------------------------- > If at first you don't succeed... > ...skydiving is not for you. > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >