From chemistry-request@server.ccl.net Sat Oct 13 09:56:44 2001 Received: from mailhub1.shef.ac.uk ([143.167.1.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9DDuiB08471 for ; Sat, 13 Oct 2001 09:56:44 -0400 Received: from ramsley.shef.ac.uk ([143.167.103.254]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 15sPHP-0003BW-00 for chemistry@ccl.net; Sat, 13 Oct 2001 14:56:43 +0100 Received: from RAMSLEY/SpoolDir by ramsley.shef.ac.uk (Mercury 1.48); 13 Oct 01 15:09:01 +0100 Received: from SpoolDir by RAMSLEY (Mercury 1.48); 13 Oct 01 15:08:54 +0100 From: "O.Nicolotti" To: chemistry@ccl.net Date: Sat, 13 Oct 2001 15:08:46 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: QSAR and scrambling Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12a) Message-Id: Hy everybody, I would like to know your opinion about scrambling the activities data for validating QSAR models. Usually, after scrambling affinity data, the classical statistics parameters (r2 and q2) are supposed to go dramatically down if the original QSAR models was a reliable model. Anyway, if you are dealing with CoMFA, I would expect bad q2 after scrambling but the r2 could also be still quite high since r2 tend to be high when the number of descriptors is very large as it is in the CoMFA grid. In other word while q2 must to go down, r2 values should not mean anything of relevant for validating the QSAR models. Any comment is very welcome. Orazio From chemistry-request@server.ccl.net Sat Oct 13 11:13:17 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9DFDHB11303 for ; Sat, 13 Oct 2001 11:13:17 -0400 Received: from trentu.ca ([204.225.12.60]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K9G83NFAVY001AS0@trentu.ca> for chemistry@ccl.net; Sat, 13 Oct 2001 11:12:29 EDT Date: Sat, 13 Oct 2001 11:13:38 -0400 From: elewars Subject: charges on sphere, another To: chemistry@ccl.net, koldham@trentu.ca Message-id: <3BC85A21.2C3B2C43@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 Oct 13 Another interesting contribution, from a new angle, to the charges on a sphere problem: ------------------------ Mitchell Polley I was about to send you this message and I saw Dr Tubert's excellent response, which made my repsonse somewhat obsolete. However, I've decided to send it anyway. Dear Dr. Lewars, If the problem is reduced to something simpler, it may provide minor insight into the the more complex picture. While pondering your original question I simplified it by getting rid of the "charges" on the points and installing instead fixed radii. Afterall, won't any two point charges of like polarity repel each other to infinty if no other forces act? So assuming the distance between two identical point charges will reach some sort of equilibrium distance (d - measured centre to centre), and assuming that this is a constant distance, we can rethink the problem as one of fixed d, similar to a spherical hardshell VDW model of atoms in close packing circumstances. Obviously, n charges seeking the equilibrium distance will form a minimum surface area aggregate (spheroid) and as n increases the packing becomes more complex. Tetrahedron -> trigonalbipyramid -> octahedron -> pentagonalbipyramid -> cube/rhombohedron -> etc. After envisioning this growth for a while you can see that after the tetrahedron we have a shape with three "slices": two "poles" and an "equator". Clearly the point at which having one of the "atoms" at the centre of the sphere comes when the radius of the aggregate, measured from the centroid to the centre of any of the "atoms", comes when r => d. Under the series envisioned above this wil be when there are 6 "atoms" in the equatorial slice hexagongally, and 3 "atoms" in each of the polar slices in a triangular arrangement - only at this point can an extra "atom" fit into the space in the middle, and the close packing be preserved (thus keeping constant d between ALL atoms in the aggregate). With this simplified approach the answer (I believe) is that the 13th "atom" goes in the middle. I'm not sure that it answers your more complex problem of equidistant charges on a spherical surface but I beleive it provides at least a different perspective on how the problem might be conceptualized. Regards, Mitchell Polley. =========================== From chemistry-request@server.ccl.net Sat Oct 13 06:02:44 2001 Received: from mailrelay1.inwind.it ([212.141.54.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9DA2iB00598 for ; Sat, 13 Oct 2001 06:02:44 -0400 Received: from mircomputer (62.98.218.62) by mailrelay1.inwind.it (5.5.029) id 3BC7162600019DB0 for chemistry@ccl.net; Sat, 13 Oct 2001 12:02:29 +0200 Message-ID: <001201c153cf$2b88b600$3eda623e@mircomputer> From: "Mirco Meniconi" To: Subject: molecular dynamic: wich program? Date: Sat, 13 Oct 2001 12:09:38 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C153DF.EE3752A0" 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 This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C153DF.EE3752A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I'm looking for a free program for bio-molecular dynamics simulations, = capable to run under a multiprocessor system. could you send me the web-addres where I can find out this program? thanks for yours help.=20 --=20 Dr. Mirco Meniconi university of Perugia (ITALY) e-mail: mirco.me@inwind.it phone +39 75 5855114 mobile +39 328 9526589 ------=_NextPart_000_000F_01C153DF.EE3752A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
I'm looking for a free program for = bio-molecular dynamics simulations, capable to run under a=20 multiprocessor system.
could you send me the web-addres = where I=20 can find out this program?
thanks for yours = help. 
--
Dr. Mirco Meniconi
university = of Perugia=20 (ITALY)
 
e-mail: mirco.me@inwind.it
phone +39 = 75=20 5855114
mobile +39 328 9526589
------=_NextPart_000_000F_01C153DF.EE3752A0-- From chemistry-request@server.ccl.net Sat Oct 13 06:41:53 2001 Received: from mail.etang.com ([202.101.42.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9DAfqB01648 for ; Sat, 13 Oct 2001 06:41:53 -0400 Received: from lizhenhua (unknown [202.108.240.3]) by mail.etang.com (Postfix) with ESMTP id D4CD91C92F553 for ; Sat, 13 Oct 2001 18:42:35 +0800 (CST) Message-ID: <003101c153d4$03cb1ea0$de0a150a@lizhenhua> From: "Zhenhua Li" To: "CCL" References: <003d01c1500c$8bf1bdf0$de0a150a@lizhenhua> Subject: Summery:exact energy of atoms or small poly-atoms Date: Sat, 13 Oct 2001 18:44:11 +0800 Organization: Chem. Dept. Fudan Univ. Shanghai, China MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Thanks for everyone: The information I obtained is that the HF limit or even CASSCF limit of atoms and diatoms can be calculated by numerical HF codes available free of charge. But it is rather difficult to obtain exact correlation energies. Several groups are developing correlation methods explicitely including correlation, i.e. inter-electron distances to calculate exact non-relativistic correlation energy. Some literatures have estimated the correlation energy of atoms by substracting experimental energies with experimentally or theoretically determined relativistic energy and HF limit. Thanks for all warm replies. Zhenhua Following is a summary of replies: Michael Nolan : there is a paper by Davidson et al, PRA 1991, vol 44, 7071, in which they present exact energies for atoms and ions thereof in the first row of the periodic table. There might be newer papers, I am not sure. elewars : Hello, I don't think there are exact solutions of the S. equation except for one-electron atoms (H, He+, ...) or molecules (like H2+). There are ways to extrapolate to the basis set limit, with various degrees of accuracy: "complete basis set" methods, CBS-4, CBS-Q, CBS-APNO (G. A. Petersson): see papers in J. Chem. Phys., book "Computational Thermochemistry", Edited by Irikura and Frurip (ACS, Washington DC, 1998). Ngai Ling Ida Ma : Not sure whether this is what you are looking for. Are you looking for full-CI benchmarks? If that is the case, you might like to check up on N.C. Handy's paper. He has a program for doing full-CI, and I remember he has several papers in JCP between 1980-1990 of these systems. I don't think he has "everything" in one paper but it should give you a start. Denny aug-cc-pv6z Frank Jensen : HF limits for atoms are in the literature. HF limits for some diatomic systems are also there, or can be generated by numerical HF programs which are available free of charge. In connection with other work I have developed some basis sets which should be able to get 10^-7 accurcy on absolute energies in a relative sense, and which can be used for polyatomic molecules. Absolute energies including electron correlation are harder to come by. Check some of the recent work on R12 methods for getting estimates for small molecules. For atoms the sum of ionization potentials give the total energy experimentally. ----- Original Message ----- From: "Zhenhua Li" To: "CCL" Sent: Monday, October 08, 2001 11:18 PM Subject: CCL:exact energy of atoms or small poly-atoms > Dear listers, > Have you any idea how to find energies of exact or close to exact (either > SCF or correlation level) one-particle basis set limit for atoms or small > poly-atoms? > Are there any exact energies of atoms or small poly-atoms (exact solution of > Schrodinger equation)? > > Li Zhenhua > > > > > -= 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 > > > > > From chemistry-request@server.ccl.net Sat Oct 13 14:09:50 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9DI9oB17684 for ; Sat, 13 Oct 2001 14:09:50 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id NAA13818 for ; Sat, 13 Oct 2001 13:07:14 -0500 (CDT) Date: Sat, 13 Oct 2001 13:07:14 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: TIP$P water model Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Thanks for all the help regarding my previous query. I incorporated the TIP4P model. I have one question regarding the constraints in this model of water. To avoid the dynamics on the dummy particle ( as suggested in the GROMACS site, thanks to David Va der Spoel and Paul van Maaren), iam redistribuiting the forces on the dummy to the other three atoms. To do this every time step, i compute the positions of the dummy particle before passing all the coordinates to Ewald method. For the constraints part, i still have constraints only on OH, OH and HH bond. Do i need constraints between dummy particle(M) and other three atoms? If i don't want to use the rigid model, can i use a flexible model for TIP4P water? Can anyone give me some information about where i can get the parameters for the flexible model of TIP4P model of water(AMBER has parameters for TIP3P, i coudn't find parameters for TIP4P.) Thanks vani