From chemistry-request@server.ccl.net Sun May 9 17:24:06 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA26084 for ; Sun, 9 May 1999 17:24:06 -0400 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA13040 Sun, 9 May 1999 17:18:23 -0400 (EDT) Received: from sandra.schrodinger.com (sandra.schrodinger.com [206.231.140.250]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id OAA18742 for ; Sun, 9 May 1999 14:21:38 -0700 Received: from localhost (shenkin@localhost) by sandra.schrodinger.com (8.8.5/8.8.5) with ESMTP id RAA06599 for ; Sun, 9 May 1999 17:17:42 -0400 X-Authentication-Warning: sandra.schrodinger.com: shenkin owned process doing -bs Date: Sun, 9 May 1999 17:17:42 -0400 (EDT) From: Peter Shenkin To: CHEMISTRY@www.ccl.net Subject: Re: CCL:clustering of a huge number of conformations In-Reply-To: <19990504230539.4811.rocketmail@web108.yahoomail.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Not all clustering methods require all pairwise similarities to be computed, but many do. One approach, if you have N conformations and N is large, is to do full N^2 clustering for, say, SQRT(N) conformations, selected randomly; then, for the rest, assign each conformation to the cluster whose centroid it is closest to. This is good to get a feeling for the ensemble, statistically, but perhaps it's not optimal to search for rare events. When you say you got 260 clusters using an alternative method rather thant the 236 you expected ("generated by the original algorithm"), it's hard to know what you mean. There's no rigorous definition of a cluster; or, better, there are lots of definitions, and in different situations different definitions better correspond with what intuition or some other algorithm picks out or defines as most reasonable. You can see our WWW pages (under MacroModel) for info about our XCluster program, which performs single-link clustering (a full N^2) process) on molecular conformations and provides tools to help interpret the results. We wouldn't be able to handle 60K confs, though. -P. On Tue, 4 May 1999, anstrom nanometer wrote: > > Dear all, > > I have a huge number of conformations to cluster (~60k). Since all > clustering algorithm that I know need to calculate pair-wise distances > between every two conformations, it will be an unsurmountable big space > for my computer's memory (14.4G). I figured out an alternative way to > implement it, but the clutering result was found not a optimal > solution, i.e. for example, 260 clusters were generated by my way > instead of the expected 236 clusters generated by the original > algorithm. > > I would appreciate receiving any of your knowledge on this subject. > > Hongyu Zhang > CARB, U. of Maryland > > > _________________________________________________________ > Do You Yahoo!? > Get your free @yahoo.com address at http://mail.yahoo.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Sat May 8 21:48:51 1999 Received: from smtp.263.net ([202.96.44.19]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA17678 for ; Sat, 8 May 1999 21:48:48 -0400 Received: (fmail 9751 invoked from network); 8 May 1999 17:39:46 -0000 Received: from unknown (HELO comkem) (202.96.76.69) by 202.96.44.19 with SMTP; 8 May 1999 17:39:46 -0000 Message-ID: <001401be9a3b$34f87a40$454c60ca@comkem> From: "yongwen" To: "CCL" Subject: On Energies of LUMO/HOMO in G94' Date: Sun, 9 May 1999 09:44:12 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0010_01BE9A00.7E5AA5E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_0010_01BE9A00.7E5AA5E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLs, I am interested in the energies of LUMO and HOMO. I can get the = orbital coefficients of them with "POP=3DREG" in Guassian94, but no = thier energies. Does anyone can help me? Can G94 give the energies of = LUMO/HOMO? If not, would you mind to instruct me which programs can do = that work? Your any kindly reply will be very appreciated. I'll summary. Thanks in advance. yongwen EMail: yongwen@263.net ------=_NextPart_000_0010_01BE9A00.7E5AA5E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLs,
 
    I am interested in the energies = of LUMO and=20 HOMO. I can get the orbital coefficients of them with = "POP=3DREG" in=20 Guassian94, but no thier energies. Does anyone can help me? Can G94 give = the=20 energies of LUMO/HOMO? If not, would you mind to instruct me which = programs can=20 do that work? Your any kindly reply will be very appreciated. I'll=20 summary.
 
    Thanks in advance.
 
yongwen
EMail: yongwen@263.net
 
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