From chemistry-request@ccl.net Tue Sep 9 02:02:02 2003 Received: from web21103.mail.yahoo.com (web21103.mail.yahoo.com [216.136.227.105]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8961UB8025400 for ; Tue, 9 Sep 2003 02:01:31 -0400 Message-ID: <20030909060119.32948.qmail~at~web21103.mail.yahoo.com> Received: from [203.90.127.102] by web21103.mail.yahoo.com via HTTP; Mon, 08 Sep 2003 23:01:19 PDT Date: Mon, 8 Sep 2003 23:01:19 -0700 (PDT) From: neda mirsamadi Subject: Flying ice cube To: chemistry~at~ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear friends I am simulating a peptide made out of 5 amino acids with GROMACS. my peptide often goes out of the box and enters from opposite side. I checked nstcomm, it is set to 1. Can I continue with the same simulation and start analysis? If not how that affects the simulation? What is the solution for that? Thanks, Neda __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From chemistry-request@ccl.net Tue Sep 9 08:11:18 2003 Received: from freeman.netbox.cz (freeman.netbox.cz [212.96.166.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h89CAkB8020834 for ; Tue, 9 Sep 2003 08:10:47 -0400 Received: from localhost (localhost [127.0.0.1]) by freeman.netbox.cz (Postfix) with ESMTP id B7CAA138E6D; Tue, 9 Sep 2003 14:04:27 +0200 (CEST) Received: from freeman.netbox.cz ([127.0.0.1]) by localhost (freeman [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 10642-06; Tue, 9 Sep 2003 14:04:27 +0200 (CEST) Received: from chemi.muni.cz (r70s10p08.home.nbox.cz [213.211.37.34]) by freeman.netbox.cz (Postfix) with ESMTP id A8FDA138E69; Tue, 9 Sep 2003 14:04:26 +0200 (CEST) Message-ID: <3F5DC343.5090204~at~chemi.muni.cz> Date: Tue, 09 Sep 2003 14:10:43 +0200 From: Lubos Vrbka Reply-To: shnek~at~chemi.muni.cz Organization: NCBR User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: neda mirsamadi , chemistry~at~ccl.net Subject: Re: CCL:Flying ice cube References: <20030909060119.32948.qmail~at~web21103.mail.yahoo.com> In-Reply-To: <20030909060119.32948.qmail~at~web21103.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new-20030314-p2 (Debian) at netbox.cz X-Spam-Status: No, hits=-1.1 required=7.0 tests=IN_REP_TO,REFERENCES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) hello, > I am simulating a peptide made out of 5 amino acids > with GROMACS. > my peptide often goes out of the box and enters from > opposite side. > I checked nstcomm, it is set to 1. > Can I continue with the same simulation and start > analysis? > If not how that affects the simulation? > What is the solution for that? i think that this doesn't affect your simulation at all as you use the box. i use amber, not gromacs, but i can see similar "problems", too. before you start your analysis you have to "image" your trajectories, i.e. to put your molecule back to the (center of the) box. i think you should have some option to "image" the trajectory in some of your post-processing or analysis programs that are part of the gromacs software package. however, it's possible that this is handled different way in amber. a very quick 'google' gave me following link; it could be helpful... http://www.gromacs.org/pipermail/gmx-users/2002-June/028523.html regards, lubos -- ################################################# Mgr. Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek~at~chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 541 129 508 ################################################# From chemistry-request@ccl.net Tue Sep 9 04:49:19 2003 Received: from mailhost1.tudelft.nl (mailhost1.tudelft.nl [130.161.180.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h898mlB8005595 for ; Tue, 9 Sep 2003 04:48:48 -0400 Received: from 127.0.0.1 (localhost [127.0.0.1]) by rav.antivirus (Postfix) with SMTP id 66C549CC for ; Tue, 9 Sep 2003 10:48:23 +0200 (CEST) Received: from mail.dct.tudelft.nl (tnw-dct1.dct.tudelft.nl [130.161.196.201]) by mailhost1.tudelft.nl (Postfix) with ESMTP id 8F82396B for ; Tue, 9 Sep 2003 10:48:22 +0200 (CEST) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 9 Sep 03 10:48:46 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 9 Sep 03 10:48:40 +0200 From: "Martijn Zwijnenburg" Organization: Delft University of Technology (TNW-DCT) To: chemistry:at:ccl.net Date: Tue, 09 Sep 2003 10:48:31 +0200 MIME-Version: 1.0 Subject: ccl: RR out of range in DoVR1. and G98 Message-ID: <3F5DAFE8.1168.6B43B146@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.11) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Spam-Status: No, hits=1.3 required=7.0 tests=FORGED_RCVD_TRAIL version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I'm trying to restart an opt calc from a lower basis-set optimized structure (gom=check, guess=check) and after the first SCF convergence the G98 calculation crashes when calculating the integral first derivatives with an "RR out of range in DoVR1." error message (see below). Anybody any clue what is the problem? Thanx in advance. Gr. Martijn Zwijnenburg Leave Link 702 at Mon Sep 8 22:54:39 2003, MaxMem= 91750400 cpu: 0.0 (Enter /opt/g98/g98/l703.exe) Compute integral first derivatives. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. RR out of range in DoVR1. Error termination via Lnk1e in /opt/g98/g98/l703.exe. ---------------------------------------------------------------------- --- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg:at:tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@ccl.net Tue Sep 9 04:38:25 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h898brB8004944 for ; Tue, 9 Sep 2003 04:37:53 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HKX0060VUN51F:at:mailserver.unimi.it> for CHEMISTRY:at:ccl.net; Tue, 09 Sep 2003 10:37:54 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HKX00DMOUN4YX:at:smtp.unimi.it> for CHEMISTRY:at:ccl.net; Tue, 09 Sep 2003 10:37:52 +0200 (MEST) Date: Tue, 09 Sep 2003 10:47:25 +0200 From: Alessandro Contini Subject: Re: CCL:solvent effect In-reply-to: <3251EC702A37B9458A01D917C3D3B389034FEF:at:sgofusr20.nac.ppg.com> To: "Deng, Jun" Cc: CHEMISTRY:at:ccl.net Message-id: <200309091047.25646.alessandro.contini:at:unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.3 References: <3251EC702A37B9458A01D917C3D3B389034FEF:at:sgofusr20.nac.ppg.com> X-Spam-Status: No, hits=-2.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h898cPB8004982 Hi Jun, see Champagne, B et all., Chem. Phys, 238 (1998) 153-163 for a good reference on PCM and the importance of optimizing with solvent. Hope this help Alessandro Contini Alle 22:09, lunedl 8 settembre 2003, Deng, Jun ha scritto: > Dear Colleagues: > I am using G98 to calculate the Gibbs free energy of the reaction in the > solvent. The reaction involve ionic species, so the solvent effect is > important. Here is what I did: > > 1. Gas phase geometry optimization and freq calculation > 2. Using PCM to calculate single point energy > 3. Add thermal correction energy from gas phase to single point energy > calculated in solvent. > > Strictly, I think it is better to do geom. optimization and freq. calc. in > solvent. However, I couldn't do this in G98 with PCM. Do you have any > experience in how important it is to calculate reaction energy with > optimized geometry and freq in solvent? > > Thanks in advance, > > Jun Deng > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Facolt` di Farmacia Universit` degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm ------------------------------------------------------------------- ------------------------------------------------------------------- This e-mail and any attachments is confidential and may contain attorney privileged information intended for the addressee(s) only. Reading, copying, disclosure or use by anybody else is unauthorised. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail. ------------------------------------------------------------------- Il contenuto di questo messaggio elettronico e' riservato e tutelato dal segreto professionale ed e' rivolto eslusivamente al/ai destinatario/i identificato/i. Pertanto e' proibito leggerlo, copiarlo, divulgarlo o utilizzarlo da parte di chiunque salvo il/i destinatario/i. Se non siete il destinatario, vi invitiamo a cancellare il messaggio ed eventuali allegati dandocene immediatamente comunicazione scritta a mezzo posta elettronica. From chemistry-request@ccl.net Tue Sep 9 09:07:24 2003 Received: from york.smtp.ru (york.smtp.ru [62.118.249.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h89D6qB8023849 for ; Tue, 9 Sep 2003 09:06:53 -0400 Received: from [193.233.4.1] (account ) by york.smtp.ru (CommuniGate Pro WebUser 3.5.9) with HTTP id 18420790 for ; Tue, 09 Sep 2003 17:06:52 +0400 From: "Ivan Fedyanin" Subject: CCL:NICS in charged molecules To: chemistry$at$ccl.net X-Mailer: CommuniGate Pro Web Mailer v.3.5.9 Date: Tue, 09 Sep 2003 17:06:52 +0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="KOI8-R" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi folks! I tried to calculate NICS values for my charged molecule and suddenly found out that it's antiaromatic in the terms of prof. Schleyer's theory. So the question is: is this method applicable for open-shell systems and excited states? Thanks/ --------------------------------- Ivan Fedyanin. From chemistry-request@ccl.net Tue Sep 9 09:35:16 2003 Received: from sunchem.chem.uga.edu (sunchem.chem.uga.edu [128.192.5.2]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h89DZCB8025948 for ; Tue, 9 Sep 2003 09:35:12 -0400 Received: (qmail 3885 invoked by uid 728); 9 Sep 2003 13:34:11 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 9 Sep 2003 13:34:11 -0000 Date: Tue, 9 Sep 2003 09:34:11 -0400 (EDT) From: Zhi-Xiang Wang To: Ivan Fedyanin cc: schleyer-.at.-chem.uga.edu, Subject: Re: CCL:NICS in charged molecules In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_OSIRUSOFT_COM,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Ivan I have applied the NICS criteria to a lot of molecules. It worked very well. Sometime, it gave ridiculous results, but this was due to the instability of wavefunction. It gives good results for open-shell molecules. However you should notice that, in contrast to the 4n + 2 rule for singlet, the aromatic triplet should have 4n pi electrons. We also calculated an open-shell singlet (JACS, 2002, 124, 14854). Hope it helps. ZX On Tue, 9 Sep 2003, Ivan Fedyanin wrote: > Hi folks! > I tried to calculate NICS values for my charged molecule > and suddenly found out that it's antiaromatic in the terms > of prof. Schleyer's theory. > So the question is: is this method applicable for > open-shell systems and excited states? > > Thanks/ > --------------------------------- > Ivan Fedyanin. > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl-.at.-ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Tue Sep 9 21:22:43 2003 Received: from smtp809.mail.sc5.yahoo.com (smtp809.mail.sc5.yahoo.com [66.163.168.188]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8A1MAB8001118 for ; Tue, 9 Sep 2003 21:22:11 -0400 Received: from cat207.cqe.northwestern.edu (HELO chem.northwestern.edu) (a-beim)at(sbcglobal.net@129.105.122.207 with plain) by smtp-sbc-v1.mail.vip.sc5.yahoo.com with SMTP; 10 Sep 2003 01:22:09 -0000 Date: Tue, 9 Sep 2003 20:22:07 -0500 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: Re: Relationships between IP, EA and electrochemistry From: Geoff Hutchison To: chemistry)at(ccl.net Content-Transfer-Encoding: 7bit Message-Id: <316780FC-E32D-11D7-81E2-000A95701B7A)at(chem.northwestern.edu> X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I'm writing up a manuscript and am trying to find a reference I know I once had that related gas-phase IP and EA values to electrochemistry. It empirically corrected for solvent effects via a linear relationship (perhaps a linear free energy relationship?). In particular, I'm interested in organic pi-conjugated type molecules, but others could work too. If anyone has leads on this article or other articles relating gas-phase IP/EA data to electrochemical measurements, I'd appreciate it. I'll be glad to summarize to the list. -Geoff -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.northwestern.edu/ From chemistry-request@ccl.net Tue Sep 9 11:20:05 2003 Received: from freeman.netbox.cz (freeman.netbox.cz [212.96.166.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h89FJXB8001382 for ; Tue, 9 Sep 2003 11:19:33 -0400 Received: from localhost (localhost [127.0.0.1]) by freeman.netbox.cz (Postfix) with ESMTP id 7934E138273; Tue, 9 Sep 2003 17:13:10 +0200 (CEST) Received: from freeman.netbox.cz ([127.0.0.1]) by localhost (freeman [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 14066-06; Tue, 9 Sep 2003 17:13:09 +0200 (CEST) Received: from chemi.muni.cz (r70s10p08.home.nbox.cz [213.211.37.34]) by freeman.netbox.cz (Postfix) with ESMTP id 41AB61381FA; Tue, 9 Sep 2003 17:13:07 +0200 (CEST) Message-ID: <3F5DEF24.9000209)at(chemi.muni.cz> Date: Tue, 09 Sep 2003 17:17:56 +0200 From: Lubos Vrbka Reply-To: shnek)at(chemi.muni.cz Organization: NCBR User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Avijit Ghosh Cc: chemistry)at(ccl.net, nedamirsamadi)at(yahoo.com Subject: Re: CCL:Flying ice cube References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new-20030314-p2 (Debian) at netbox.cz X-Spam-Status: No, hits=-2.1 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > Avijit Ghosh wrote: > Out of curiousity, is there a way in gromacs to > subtract out the CM degrees of freedom (translational and > rotational) in the beginning of the simulation? I'm guessing > thats what you are seeing. as i stated before, i don't use gromacs... but quick 'google' gave me the following: http://www.gromacs.org/pipermail/gmx-users/2002-June/028384.html (i used following keywords: remove degrees of freedom gromacs); gromacs mailing lists and online documentation could help, too... regards, lubos -- ################################################# Mgr. Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek)at(chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 541 129 508 ################################################# From chemistry-request@ccl.net Tue Sep 9 11:47:35 2003 Received: from einstein.physics.drexel.edu (einstein.physics.drexel.edu [129.25.7.60]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h89Fl3B8003236 for ; Tue, 9 Sep 2003 11:47:04 -0400 Received: from silicon (silicon.physics.drexel.edu [129.25.8.33]) by einstein.physics.drexel.edu (8.11.6/8.11.6) with ESMTP id h89FiQm13835; Tue, 9 Sep 2003 11:44:26 -0400 Date: Tue, 9 Sep 2003 11:47:01 -0400 (EDT) From: Avijit Ghosh To: Lubos Vrbka cc: chemistry)at(ccl.net, Subject: Re: CCL:Flying ice cube In-Reply-To: <3F5DEF24.9000209)at(chemi.muni.cz> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Tue, 9 Sep 2003, Lubos Vrbka wrote: > > Avijit Ghosh wrote: > > Out of curiousity, is there a way in gromacs to > > subtract out the CM degrees of freedom (translational and > > rotational) in the beginning of the simulation? I'm guessing > > thats what you are seeing. > > as i stated before, i don't use gromacs... but quick 'google' gave me > the following: > http://www.gromacs.org/pipermail/gmx-users/2002-June/028384.html > (i used following keywords: remove degrees of freedom gromacs); gromacs > mailing lists and online documentation could help, too... Ahh apologies I think i replied to the wrong person. I had originally meant to apply to the person who posed the question w/ regards to the "flying" cube. -avi