From chemistry-request@ccl.net Tue Oct 5 23:59:06 2004 Received: from mail.monmouth.edu (mail.monmouth.edu [192.100.64.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i964x5qw012281 for ; Tue, 5 Oct 2004 23:59:05 -0500 Received: from hawkmail.monmouth.edu (hawkmail.monmouth.edu [10.11.0.5]) by mail.monmouth.edu (8.12.11/8.12.11) with SMTP id i965ALiC023135; Wed, 6 Oct 2004 01:10:23 -0400 Received: from 67.82.187.169 (SquirrelMail authenticated user rtopper) by hawkmail.monmouth.edu with HTTP; Wed, 6 Oct 2004 01:10:23 -0400 (EDT) Message-ID: <1584.67.82.187.169.1097039423.squirrel:at:hawkmail.monmouth.edu> Date: Wed, 6 Oct 2004 01:10:23 -0400 (EDT) Subject: ECCC10 Preliminary Announcement From: "Robert Topper" To: chemistry:at:ccl.net Cc: rtopper:at:monmouth.edu User-Agent: SquirrelMail/1.4.2 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 Importance: Normal X-Scanned-By: MIMEDefang 2.43 X-Spam-Status: No, hits=4.3 required=7.5 tests=PRIORITY_NO_NAME, RCVD_IN_DYNABLOCK,RCVD_IN_NJABL,RCVD_IN_NJABL_DIALUP,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Preliminary ECCC10 Announcement Dear colleagues, I am pleased to announce that the 10th Electronic Computational Chemistry Conference will be held during the month of April 2005, entirely on the Internet, at http://eccc.monmouth.edu. A call for papers will follow this announcement in the very near future. As in previous years, ECCC10 is a multidisciplinary, international conference and covers all aspects of computational and theoretical chemistry and materials science, as well as computational molecular biology, computational and theoretical molecular and atomic physics, visualization, chem- and bio-informatics, the history of computational chemistry and related fields. Participants will be able to view the presentations and discuss them entirely through a web browser. As with the previous nine ECCCs, ECCC10 will have NO registration fee and is a completely virtual, online conference. The ECCC was originally conceived of and developed by Steven Bachrach, who organized the first five meetings. Abstracts for all contributions to ECCC10 will be reviewed by the Scientific Organizing Committee (SOC) to insure novelty, scientific value, and appopriateness for inclusion in the conference. Invitations to join the SOC will be issued shortly; volunteers who would like to help with various aspects of the conference (including volunteers for SOC membership) would be most welcome. All presentations must be made in HTML format and ideally will take full advantage of the interactive nature of the World-Wide Web to present their findings and conclusions. Authors may choose to either serve their contributions from their own local web site, or may request us to serve them from our own server. Uploaded contributions will be removed from our server at the end of ECCC10. As in ECCC9, a single weeklong "interactive" session will be part of the conference. This session will be held via asynchronous posting of questions to the conference site, which authors can choose to receive either at the site, at their personal email account, or both. All authors must commit to having at least one coauthor available to answer questions (i.e. by checking the discussion board at least once daily) during the "interactive" session to provide timely responses (within approximately 24 hours) to any questions that conferees may have about their online presentation. I very much look forward to your active participation in ECCC10. Robert Q. Topper Department of Chemistry, Medical Technology and Physics Monmouth University West Long Branch, NJ rtopper:at:monmouth.edu http://eccc.monmouth.edu From chemistry-request@ccl.net Wed Oct 6 10:11:23 2004 Received: from web52009.mail.yahoo.com (web52009.mail.yahoo.com [206.190.39.65]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i96FBMwi010010 for ; Wed, 6 Oct 2004 10:11:22 -0500 Message-ID: <20041006150007.29980.qmail^at^web52009.mail.yahoo.com> Received: from [128.112.141.35] by web52009.mail.yahoo.com via HTTP; Wed, 06 Oct 2004 08:00:06 PDT Date: Wed, 6 Oct 2004 08:00:06 -0700 (PDT) From: Konstantin Kudin Subject: Re: CCL:Guess on change in geometry To: Matt Challacombe , chemistry^at^ccl.net In-Reply-To: <200410050911.09635.MChalla^at^ICE.LANL.GOV> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Matt, There could be a number of ways to get density for an updated geometry. Perhaps, the easiest ones would be to purify the previous density matrix, or diagonalize the old Fock matrix with the new orbitals. The geometry changes should not be too large. Specifically: 1) density purification - Diagonalize {-SV*D*(SV)^t} where D is the old atomic density, S, V are new overlap and orthonormal basis coefficient matrices. Occupy Ne lowest eigenvalues. That is what {-} is for. With the {-}, 1 becomes -1 and everything is sorted by the diagonalization routine itself. 2) old Fock diagonalization - Diagonalize {V^t*F*V}, where F is the old Fock matrix, V is a new orthonormal coefficient matrix. As before, occupy Ne lowest eigenvalues. {^t} stands for complex-conjugate. My experience would suggest that 1) appears to be better than 2), although if the gain is significant or marginal I am still not fully sure. I have used 2) a lot with the periodic boundary conditions calculations. On the other hand, 1) worked like a charm when I needed to create a good density matrix from ionic densities, then D consisted of patches for ionic densities with 0s for cross-ionic density elements. Such "patching" permits one to keep the ionic electronic state for transition metals. Kostya --- Matt Challacombe wrote: > Hi, > > I haven't seen much in the quantum chemistry literature on methods > for > creating a new guess to start an SCF after a change in geometry. I'm > guessing > this is something that most code developers take for granted, and > never really > publish. Do any of you CCL'ers out there have the intimate details > of these > procedures for your code of choice? > > Thx, Matt > > -- > Matt Challacombe, Group T-12, LANL > MChalla^at^LANL.Gov, (505) 665-5905 > http://www.t12.lanl.gov/~mchalla/ > _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From chemistry-request@ccl.net Wed Oct 6 10:01:01 2004 Received: from pernis.its.uu.se (pernis.its.UU.SE [130.238.4.153]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i96F0xwi009429 for ; Wed, 6 Oct 2004 10:01:00 -0500 Received: by pernis.its.uu.se (Postfix, from userid 205) id 98FC2945; Wed, 6 Oct 2004 17:12:18 +0200 (MSZ) Received: from pernis.its.uu.se(127.0.0.1) by pernis.its.uu.se via virus-scan id s1149; Wed, 6 Oct 04 17:11:07 +0200 Received: from [130.238.236.136] (kemi136.kemi.uu.se [130.238.236.136]) (using TLSv1 with cipher RC4-SHA (128/128 bits)) (No client certificate requested) by pernis.its.uu.se (Postfix) with ESMTP id 0EA29336 for ; Wed, 6 Oct 2004 17:11:07 +0200 (MSZ) Mime-Version: 1.0 (Apple Message framework v619) Message-Id: Content-Type: text/plain; charset=WINDOWS-1252; format=flowed To: chemistry^at^ccl.net From: Torben Rasmussen Subject: CCL:Summary: Hydrophobic surface area Date: Wed, 6 Oct 2004 17:16:35 +0200 X-Mailer: Apple Mail (2.619) X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i96F11wi009439 Hi, I would like to thank a series of people for very valuable pointers about hydrophobic surface area evaluation. The people are (in no prioritized order): Mitchell Polley, Jamie Platts, Andreas Bender, Joe, Rajarshi Guha, Giulio Vistoli, Gabriele Cruciani, and Michel Petitjean. I haven t had a chance to test the various alternatives yet, so I might get back to some of you to obtain the scripts and code that you have kindly offered to provide me with. I think, that I will initially test GRID, but I may eventually also test some of the other proposed alternatives. Thanks again, Torben. Here are all the answers I received: Mitchell Polley: I'd recommend MolCAD by Jurgen Brickman, available from Tripos Inc. (www.tripos.com) Jamie Platts: I can send a copy of Dodd and Theorodou's original VOLUME program, which treats molecules as a set of super-imposed vdw spheres and reports their exposed surface area (see reference below). We've also modified this to read MDL mol files, and automatically identify polar (N, O, NH, OH) atoms, if this would be useful. Both are freely distributed under the GNU GPL. Reference: "Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes" L.R. Dodd and D.N. Theodorou MOLECULAR PHYSICS, Volume 72, Number 6, 1313-1345, April 1991 Andreas Bender: One possibility is GRID (http://www.moldiscovery.com/) - which is free for academic research groups. You can calculate points on the surface e.g. using msms and then use the coordinates as input for GRID, in combination with suitable probes (e.g. methyl or DRY probe in your case) put at those points you get estimates about "hydrophobicity" (energy values) in certain areas of your molecule. I wrote a tcsh script to calculate those energy values in bath mode and I could send it to you. Just be aware that you need to have msms and GRID installed for it to run. Joe: One of the easiest approaches is to take Ertl's TPSA rules to calculate polar surface area and consider everything else as lipophilic (total area - TPSA). If you want graphical representations, I think Molcad does this... Rajarshi Guha: HSA descriptors (as well as surface area and molecular volume) are available in the ADAPT package (http://research.chem.psu.edu/pcjgroup/) Giulio Vistoli: I can suggest to use VEGA program (www.ddl.unimi.it) It is free and can calculate polar surface area and total area and by difference you can have an evaluation of hydrophobic surface. Gabriele Cruciani: Try GRID, with DRY (hydrophobic) probe, for small molecules and biomolecules as well. It is free. Windows UNIX and Linux are available, under www.moldiscovery.com Michel Petitjean: Look to the freeware ASV (there is documentation and references): http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Both the analytical method and the Monte-Carlo are included. From chemistry-request@ccl.net Wed Oct 6 17:13:47 2004 Received: from hotmail.com (bay4-dav4.bay4.hotmail.com [65.54.170.108]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i96MDknE012529 for ; Wed, 6 Oct 2004 17:13:46 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 6 Oct 2004 15:25:03 -0700 Received: from 67.41.169.179 by BAY4-DAV4.phx.gbl with DAV; Wed, 06 Oct 2004 22:24:12 +0000 X-Originating-IP: [67.41.169.179] X-Originating-Email: [rwoodphd~at~msn.com] X-Sender: rwoodphd~at~msn.com From: "Richard Wood" To: Subject: FREE MD software Date: Wed, 6 Oct 2004 16:24:11 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0025_01C4ABC0.E980A810" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Message-ID: X-OriginalArrivalTime: 06 Oct 2004 22:25:03.0515 (UTC) FILETIME=[533D5EB0:01C4ABF3] X-Spam-Status: No, hits=4.2 required=7.5 tests=HTML_40_50,HTML_MESSAGE, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS,SUBJ_FREE_CAP,SUB_FREE_OFFER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0025_01C4ABC0.E980A810 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all Can anyone point me to some free software to do molecular dynamics = simulations that run or runs under Windows (preferably), Cygwin or = Linux? I'd prefer Windows programs, but the other two would work as = well. I'm on a real low budget, so I really need some free programs. Thanks in advance, Richard ------=_NextPart_000_0025_01C4ABC0.E980A810 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all
 
Can anyone point me to some free = software to do=20 molecular dynamics simulations that run or runs under Windows = (preferably),=20 Cygwin or Linux?  I'd prefer Windows programs, but the other two = would work=20 as well.  I'm on a real low budget, so I really need some free=20 programs.
 
Thanks in advance,
Richard
 
 
------=_NextPart_000_0025_01C4ABC0.E980A810-- From chemistry-request@ccl.net Wed Oct 6 20:53:47 2004 Received: from smtp3.es.uci.edu (smtp3.es.uci.edu [128.200.80.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i971rjqt028654 for ; Wed, 6 Oct 2004 20:53:46 -0500 Received: from heathbo (ppp-68-122-211-13.dsl.irvnca.pacbell.net [68.122.211.13]) (authenticated bits=0) by smtp3.es.uci.edu (8.12.8/8.12.8) with ESMTP id i9724shY022733 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Wed, 6 Oct 2004 19:04:56 -0700 X-UCInetID: masa Message-ID: <001401c4ac11$5e509f60$0dd37a44@heathbo> From: "Masa Watanabe" To: "Richard Wood" , References: Subject: Re: CCL:FREE MD software Date: Wed, 6 Oct 2004 19:00:04 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C4ABD6.B07D01B0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 Disposition-Notification-To: "Masa Watanabe" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=6.3 required=7.5 tests=HTML_50_60,HTML_MESSAGE,MY_DSL, RCVD_IN_DSBL,RCVD_IN_DYNABLOCK,RCVD_IN_NJABL,RCVD_IN_NJABL_DIALUP, RCVD_IN_SORBS,SUBJ_FREE_CAP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C4ABD6.B07D01B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RIchard, The following two programs should be what you are looking for: Tinker: http://dasher.wustl.edu/tinker/ NAMD: http://www.ks.uiuc.edu/Research/namd/ Masa Watanabe ----- Original Message -----=20 From: Richard Wood=20 To: CHEMISTRY|at|ccl.net=20 Sent: Wednesday, October 06, 2004 3:24 PM Subject: CCL:FREE MD software Hi all Can anyone point me to some free software to do molecular dynamics = simulations that run or runs under Windows (preferably), Cygwin or = Linux? I'd prefer Windows programs, but the other two would work as = well. I'm on a real low budget, so I really need some free programs. Thanks in advance, Richard ------=_NextPart_000_0011_01C4ABD6.B07D01B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
RIchard,
 
The following two programs should be = what you are=20 looking for:
 
Tinker: http://dasher.wustl.edu/tinker/<= /A>
NAMD: http://www.ks.uiuc.edu/Res= earch/namd/
 
Masa Watanabe
 
----- Original Message -----
From:=20 Richard = Wood=20
Sent: Wednesday, October 06, = 2004 3:24=20 PM
Subject: CCL:FREE MD = software

Hi all
 
Can anyone point me to some free = software to do=20 molecular dynamics simulations that run or runs under Windows = (preferably),=20 Cygwin or Linux?  I'd prefer Windows programs, but the other two = would=20 work as well.  I'm on a real low budget, so I really need some = free=20 programs.
 
Thanks in advance,
Richard
 
 
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