From chemistry-request@www.ccl.net Fri Feb 5 02:55:37 1999 Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA22380 Fri, 5 Feb 1999 02:55:36 -0500 (EST) Received: from physics.ucsd.edu (physics.ucsd.edu [132.239.69.26]) by mailbox2.ucsd.edu (8.9.1a/8.9.1) with SMTP id XAA28182; Thu, 4 Feb 1999 23:55:33 -0800 (PST) Received: from localhost by physics.ucsd.edu (SMI-8.6/SMI-SVR4) id XAA08386; Thu, 4 Feb 1999 23:53:48 -0800 Date: Thu, 4 Feb 1999 23:53:48 -0800 (PST) From: Margaret Cheung X-Sender: cheung@physics To: kynn@panix.com cc: chemistry@www.ccl.net Subject: Re: CCL:G:Histogram method, redux In-Reply-To: <199902042041.PAA20610@panix3.panix.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, KJ, Thank you for raising such a fun topic to discuss about. I guess there are some ideas needed to be carefully defined. 1. If the folding is "perfectly" two-state like behavior, and both the unfolded and folded states are locally stable on the energy landscape, then the free energy diagram should have a double well like feature as a function of some order parameters, such as radius of gyration, contact numbers, or number of hydrogen bonds formation etc. Such a feature which follows distinct two-state behaviors should be considered as the first order phase transition. The transition temperature, also the folding temperature (Tf) in this case, will be very sharp and smoothed out by the finite size effect. The signature of Tf could be also obtained by observing the variation of fluctuations in the energys, specific heat, from the simulation. So, by plotting Cv vs T, you can still get Tf from the energy output from the simulation. 2. Your argument 4 can not be led to argument 5. What you observed in the simulation was related to the stability between the folded and the unfolded states under various temperature. It is the signature of the first order phase transition to have such a free energy profile--when temperature is low, configuration space was trapped around the folded state on the energy landscape and the MFPT (mean first passage time) for such a configuration to escape from this local minumum is indeed very long. The result you had will be more related to the identification of where transition states are along the reaction coordinates, instead of the determination of thermodynamic value Tf. More comments are welcomed. Regards, Margaret S. Cheung Physics/Biophysics Department 0350 University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0350 On Thu, 4 Feb 1999 kynn@panix.com wrote: > > > > Thanks for the replies to my earlier query about the histogram method. > I have attempted to read some of the references suggested (given > below, for those interested, along with other references requested), > but I must confess that I can barely understand them. Before spending > any more time trying to make sense of them, it would be wise to > determine whether these methods would actually serve my purposes. So > here I give a schematic description of the problem I'm dealing with, > in the hope that someone may be able to tell me whether the "multiple > histogram method" would be of any use. > > Consider a model of protein folding dynamics, with the following > features: > > 1. The folding is perfectly two-state, the two states being designated > U (unfolded) and F (folded). Moreover, the two states are well > separated in terms of energy; i.e., if we were able to produce an > energy histogram at the folding transition temperature (Tf), the > distribution would be distinctly bimodal, with a largely unpopulated > region separating the peaks corresponding to F and U. > > 2. Let t_F(T) and t_U(T) be the mean passage times for the folding > (U->F) and the unfolding (F->U) transitions, respectively, as > functions of the temperature T. > > 3. We distinguish three temperature regimes I < II < III. In regime > I, for all practical purposes, t_U(T) is infinite, while t_F(T) is > "reasonably small". Conversely, in regime III, t_F(T) is practically > infinite, while t_U(T) is small. > > 4. In regime II, a narrow neighborhood of the folding transition > temperature Tf, both t_F(T) and t_U(T) are roughly equal, and both are > extremely large (of the order of 2-3 CPU-weeks on our workstations). > > (Of course, no sharp boundaries separate these three temperature > regimes; t_F(T) and t_U(T) grow rapidly, as one approaches regime II > from regime I and III, respectively.) > > 5. Because of the slowing down described in 4, it is extremely > difficult to determine Tf. > > The single histogram method (which I described in my original post) > would require a single run near Tf, long enough to sample both the F > and U states in a way that actually reflects their relative > probabilities. For the reason mentioned in (4) and (5) this is > impractical, which seems to rule out this method. > > But it was suggested by a few responders to my earlier post that the > *multiple* histogram method may be useful in this case. The only way > I can see to apply this method is by producing two histograms, one at > temperature T1 in regime I to sample F, and one at temperature T3 in > regime III to sample U. Then, if we "absorb" the temperature into the > definition of the Hamiltonian (as Ferrenberg and Swendsen do, see > reference below), then this could be construed a case of having two > "Hamiltonians", H/(k*T1) and H/(k*T2), (where H is the actual > Hamiltonian, in the standard nomeclature). Then I would use the > method of Bennett (see reference below) to obtain a free energy > difference between these two states (as a function of T). Is this > correct? > > (The method of Ferrenberg and Swendsen is a generalization of > Bennett's method to more than two histograms, if I've understood them > correctly). > > These multiple histogram methods require a certain amount of overlap > between the histograms, which leads, for the system described above, > to a somewhat paradoxical situation: the greater the overlap between > the two states (meaning that neither P(U;T)/P(F;T) nor P(F;T)/P(U;T) > is too small), the closer the simulation temperatures have to be to > Tf, and therefore the longer it would take to adequately sample the > phase space (as remarked in (4) above). This suggests that the > multiple histogram method would not be very useful either. Am I > right? > > Thanks for your patience. Below are the references mentioned above. > Regards, > > KJ > > From chemistry-request@www.ccl.net Fri Feb 5 05:34:42 1999 Received: from scsx01.sc.ehu.es (scsx01.sc.ehu.es [158.227.150.40]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA22885 Fri, 5 Feb 1999 05:33:51 -0500 (EST) Received: from scox01.sc.ehu.es (scox01.sc.ehu.es [158.227.150.10]) by scsx01.sc.ehu.es (8.8.4/8.7.3) with ESMTP id LAA07120 for ; Fri, 5 Feb 1999 11:32:28 +0100 (MET) Status: N Received: from sq.ehu.es (pobmelat@sqpx94.sq.ehu.es [158.227.108.94]) by scox01.sc.ehu.es (8.8.5/8.7.3) with ESMTP id LAA31554 for ; Fri, 5 Feb 1999 11:32:27 +0100 (MET) Sender: pobmelat@sc.ehu.es Message-ID: <36BACA29.10A8C4F2@sq.ehu.es> Date: Fri, 05 Feb 1999 11:38:33 +0100 From: Txema Mercero Reply-To: pobmelat@sq.ehu.es Organization: E.H.U. X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.34 i586) X-Accept-Language: Spanish, es, en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: *.WFN files with g98 and windows --> linux migration ... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL readers, I would like to make you a couple of questions: Using g98, I want to get the wavefunction in a *.wfn file. With g94 I just had to specify the output=wfn command and the name of the file at the end of the input. According to the g98 manual, the same thing should be enough for g98, however, I am trying it and I don t get the wavefunction, does anybody know which is the problem? And the second question, we are changing our operating system from Windows to Linux, we have been able to read most of the windows files we had with linux based programs, however we have a problem with the articles database. We used Reference Manager to sort our database, and know we would like to read this database with a linux based database. Does anybody know any database which works under linux, and might be able to read a database created using Reference Manager? Thank you all! Txema Mercero Grad. Student Euskal Herriko Unibertsitatea From chemistry-request@www.ccl.net Fri Feb 5 05:55:11 1999 Received: from moorea.uni-muenster.de (MOOREA.UNI-MUENSTER.DE [128.176.126.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA23021 Fri, 5 Feb 1999 05:55:07 -0500 (EST) Received: from localhost (chan@localhost) by moorea.uni-muenster.de (8.8.7/8.7.5) with ESMTP id KAA03500 for ; Fri, 5 Feb 1999 10:54:58 GMT Date: Fri, 5 Feb 1999 11:54:54 +0100 (MEZ) From: "Jerry C.C. Chan" To: chemistry@www.ccl.net Subject: Calculations of Co-59 e2qQ/h In-Reply-To: <199901271004.LAA05878@sg10.chem.tue.nl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I would be grateful if anyone of you could give me pointers to articles concerning calculations (ab initio or empirical) of quadrupolar coupling constants of cobalt-59 systems. Many thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@uni-muenster.de * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** From chemistry-request@www.ccl.net Fri Feb 5 08:44:56 1999 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA24468 Fri, 5 Feb 1999 08:44:55 -0500 (EST) Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA11451; Fri, 5 Feb 1999 08:45:49 -0400 Received: by iris.nybc.org (980427.SGI.8.8.8/940406.SGI.AUTO) id IAA11253; Fri, 5 Feb 1999 08:38:05 -0500 (EST) From: "Asim Kumar Debnath" Message-Id: <9902050838.ZM211224@iris.nybc.org> Date: Fri, 5 Feb 1999 08:38:04 -0500 In-Reply-To: Steven.Creve@dsm-group.com "CCL:CCL:CoMFA software" (Feb 2, 9:31am) References: <"36B6B6C2.10DD.1586.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Steven.Creve@dsm-group.com, CHEMISTRY@www.ccl.net Subject: Re: CCL:CCL:CoMFA software Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Steven: Please look at http://www.tripos.com/fhome2.html where it describes about QSAR with CoMFA. Hope this helps. Asim -- ======================================================================= *** *** Asim K. Debnath, Ph.D. **** Assistant Member **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@server.nybc.org ************** ======================================================================== From chemistry-request@www.ccl.net Fri Feb 5 09:38:04 1999 Received: from bclcl1.im.battelle.org (bclcl1.im.battelle.org [131.167.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA25794 Fri, 5 Feb 1999 09:38:03 -0500 (EST) Received: from ns-pandora.im.battelle.org by BCLCL1 (PMDF V5.1-10 #U2779) with ESMTP id <01J7DOWIUNDC8X1PMA@BCLCL1> for chemistry@www.ccl.net; Fri, 5 Feb 1999 09:37:51 EST Received: by ns-pandora.im.battelle.org with Internet Mail Service (5.5.1960.3) id <1BXTA45S>; Fri, 05 Feb 1999 09:38:15 -0500 Content-return: allowed Date: Fri, 05 Feb 1999 09:38:14 -0500 From: "Risser, Steve" Subject: periodic boundary conditions with DFT To: "'chemistry@www.ccl.net'" Message-id: <5913080CA46DD111A98200A0C9960C10967C7B@ns-bco-mse7.im.battelle.org> X-Mailer: Internet Mail Service (5.5.1960.3) Hi All Does anyone know of any existing DFT code that can perform calculations on periodic systems, explicitly including symmetry? Thanks. Steve ---------------------------------------------------------------------------- ------------------------ Dr. Steven M Risser Current Year Associate Professor of Physics Polymer Center Texas A&M University-Commerce Battelle Memorial Institute Commerce TX 75429 505 King Avenue Columbus, OH 43201-2693 (614) 424-3715 ---------------------------------------------------------------------------- ----------------------- From chemistry-request@www.ccl.net Fri Feb 5 09:59:16 1999 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.20.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA26140 Fri, 5 Feb 1999 09:59:15 -0500 (EST) Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA (8.8.8/8.8.8) with SMTP id JAA06908 for ; Fri, 5 Feb 1999 09:59:15 -0500 (EST) Date: Fri, 5 Feb 1999 09:59:14 -0500 (EST) From: "C.F. Matta" To: ccl Subject: Scanning Probe Microscopy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, First: I would much appreciate if you could point to me recent publications about modeling/computational studies of the interaction of the tip with the substrate in Atomic Force Microscopy (AFM) or/and Scanning Tunneling Microscopy (STM). Second: In STM, a typical separation from the tip to the substarte is 3-10 A, i.e. the tails of the wavefunctions of the tip and of the substrate are crucial. Gaussian functions are not behaving physically at long distances. Moreover, if the substrate consists of different atoms described with basis functions decaying at different rates, this will overemphasize the peacks due to the one decaying slower (the true wavefunction decays at a single rate). The Linearized Augmented PlaneWave method (LAPW), due to Tersoff & Hamann, is supposed to remedy for this. (1) Is there other methods better than LAPWD? (2) Can one implement LAPWD in, say GAUSSIAN or GAMESS? (3) If the answer to (2) is YES, then HOW? (4) If NO, then what program(s) implements this method? (5) Other suggestions? Thank you all very much. I will summarize. Cherif ....................................................................... Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ....................................................................... From chemistry-request@www.ccl.net Fri Feb 5 11:37:37 1999 Received: from chemvx.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA28098 Fri, 5 Feb 1999 11:37:36 -0500 (EST) Received: from mail.chem.tamu.edu ([165.91.67.137]) by chemvx.chem.tamu.edu (Netscape Mail Server v2.02) with ESMTP id AAA174; Fri, 5 Feb 1999 10:39:44 -0600 Message-ID: <36BB1EF7.1ED8D745@mail.chem.tamu.edu> Date: Fri, 05 Feb 1999 10:40:23 -0600 From: plin@mail.chem.tamu.edu (Ping Lin) X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Chemistry , Andreas Goeller , "Dr. Robert K. Szilagyi" Subject: Summary: references and suggestions on theoretical ET study Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Here is the summary for my question about the references on ET study, only two responses point out some, a lot less than I expected. If any one still have other suggestion, I would be very happy to summarize again. Thanks, Ping Lin Response 1: ---- Nicolas FERRE Laboratoire de Chimie Theorique Universite Henri Poincare Nancy 1 BP 239 E-mail : ferre@lctn.u-nancy.fr 54506 VANDOEUVRE-LES-NANCY Cedex _______________ If you would consider some dynamical properties of quantum particle as electron transfer, I suggest you to read some papers of Bala. He solves time-dependant Shrodinger equation for a quantum particle in a time-independant potential given by hybrid quantum-classical or pure quantum method (Valence Bond). Here is some references : * P. Bala, P. Grochowski, B. Lesyng and J.A. McCammon "Quantum-Classical Molecular Dynamics. Models and Applications" in "Quantum Mechanical simulation methods for studying biological systems" (1995) Springer * P. Bala, P. Grochowski, B. Lesyng and J.A. McCammon "Quantum-Classical Molecular Dynamics of Proton Transfer Processes in Molecular Complexes and in Enzymes" J.Phys.Chem., 100 (7) 2535-2545 Response 2: ------ Wai-To Chan Department of Chemistry York University, Toronto Ontario, Canada ________________ Here is a recent paper about electron transfer study I happen to know of. "Electron tunneling in quasi-one-dimensional resonant molecular systems. Ab initio study." Heifets, Daizadeh, Guo and Alexei A. Stuchebrukhov Journal of physcial chemistry, vol 102, pg 2847 (1998). ---------------------------------- Thanks to all those responsed. From chemistry-request@www.ccl.net Fri Feb 5 12:47:09 1999 Received: from mailgw.cc.uga.edu (mailgw.cc.uga.edu [128.192.1.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA00894 Fri, 5 Feb 1999 12:47:08 -0500 (EST) Received: from rock.ucns.uga.edu by mailgw.cc.uga.edu (LSMTP for Windows NT v1.1b) with SMTP id <0.007ED4A7@mailgw.cc.uga.edu>; Fri, 5 Feb 1999 12:47:10 -0500 Received: from localhost (stewart@localhost) by rock.ucns.uga.edu (8.9.1/8.9.1) with ESMTP id MAA27600 for ; Fri, 5 Feb 1999 12:47:09 -0500 (EST) X-Authentication-Warning: rock.ucns.uga.edu: stewart owned process doing -bs Date: Fri, 5 Feb 1999 12:47:09 -0500 From: David Stewart X-Sender: stewart@rock.ucns.uga.edu To: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:Histogram method, redux (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am forwarding this to the list on behalf of my colleague, Alan Ferrenberg. From: Alan M. Ferrenberg Subject: Re: CCL:G:Histogram method, redux (fwd) ------------------------------------------------------------------------- > Date: Thu, 4 Feb 1999 15:41:42 -0500 (EST) > From: kynn@panix.com > To: chemistry@www.ccl.net > Subject: CCL:G:Histogram method, redux > Sender: Computational Chemistry List > > > > > Thanks for the replies to my earlier query about the histogram method. > I have attempted to read some of the references suggested (given > below, for those interested, along with other references requested), > but I must confess that I can barely understand them. Before spending > any more time trying to make sense of them, it would be wise to > determine whether these methods would actually serve my purposes. So > here I give a schematic description of the problem I'm dealing with, > in the hope that someone may be able to tell me whether the "multiple > histogram method" would be of any use. > > Consider a model of protein folding dynamics, with the following > features: > > 1. The folding is perfectly two-state, the two states being designated > U (unfolded) and F (folded). Moreover, the two states are well > separated in terms of energy; i.e., if we were able to produce an > energy histogram at the folding transition temperature (Tf), the > distribution would be distinctly bimodal, with a largely unpopulated > region separating the peaks corresponding to F and U. > > 2. Let t_F(T) and t_U(T) be the mean passage times for the folding > (U->F) and the unfolding (F->U) transitions, respectively, as > functions of the temperature T. > > 3. We distinguish three temperature regimes I < II < III. In regime > I, for all practical purposes, t_U(T) is infinite, while t_F(T) is > "reasonably small". Conversely, in regime III, t_F(T) is practically > infinite, while t_U(T) is small. > > 4. In regime II, a narrow neighborhood of the folding transition > temperature Tf, both t_F(T) and t_U(T) are roughly equal, and both are > extremely large (of the order of 2-3 CPU-weeks on our workstations). > > (Of course, no sharp boundaries separate these three temperature > regimes; t_F(T) and t_U(T) grow rapidly, as one approaches regime II > from regime I and III, respectively.) > > 5. Because of the slowing down described in 4, it is extremely > difficult to determine Tf. > > The single histogram method (which I described in my original post) > would require a single run near Tf, long enough to sample both the F > and U states in a way that actually reflects their relative > probabilities. For the reason mentioned in (4) and (5) this is > impractical, which seems to rule out this method. > > But it was suggested by a few responders to my earlier post that the > *multiple* histogram method may be useful in this case. The only way > I can see to apply this method is by producing two histograms, one at > temperature T1 in regime I to sample F, and one at temperature T3 in > regime III to sample U. Then, if we "absorb" the temperature into the > definition of the Hamiltonian (as Ferrenberg and Swendsen do, see > reference below), then this could be construed a case of having two > "Hamiltonians", H/(k*T1) and H/(k*T2), (where H is the actual > Hamiltonian, in the standard nomeclature). Then I would use the > method of Bennett (see reference below) to obtain a free energy > difference between these two states (as a function of T). Is this > correct? > > (The method of Ferrenberg and Swendsen is a generalization of > Bennett's method to more than two histograms, if I've understood them > correctly). > > These multiple histogram methods require a certain amount of overlap > between the histograms, which leads, for the system described above, > to a somewhat paradoxical situation: the greater the overlap between > the two states (meaning that neither P(U;T)/P(F;T) nor P(F;T)/P(U;T) > is too small), the closer the simulation temperatures have to be to > Tf, and therefore the longer it would take to adequately sample the > phase space (as remarked in (4) above). This suggests that the > multiple histogram method would not be very useful either. Am I > right? > > Thanks for your patience. Below are the references mentioned above. > Regards, > > KJ > As much as I'd like to push the merits of multiple histograms for this problem, there are actually some much more efficient approaches that you might want to consider. The "multicanonical" simulation method was designed to work well for magnetic systems with probabilitiy distributions that have the same features as your distributions of folding states. In the multicanonical approach, instead of simulating at different temperatures and combining the results later (like the F-S multihistogram method), you bias your sampling with a distribution function that preferentially samples in the "dead area" between the two peaks. This allows the simulation to cross from one state to the other without a huge free-energy barrier. The result is that the mean passage times are dramatically reduced. With some experimentation, you can get a reasonably flat distribution of states, and then the passage from one state to the other is like a random walk. To get back to the canonical ensemble, you reweight this "flat" distribution using the inverse of the biasing function. Here are some references to early papers describing the multicanonical method: B. Berg and T. Neuhaus, Phys. Lett. B267, 249 (1991). B. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992). B. Berg, U. Hansmann and T. Neuhaus, Z. Phys. B90, 229 (1993). W. Janke, B. Berg and M. Katoot, Nucl. Phys. B382, 649 (1992). There have been more recent papers, but these should be enough to give you a feel for the method and decide if it will meets your needs. Happy reweighting! amf *************************************************************************** Alan M. Ferrenberg (amf@arches.uga.edu) Academic Professional, University Computing and Networking Services Adjunct Asst. Professor, Department of Physics Computational Physics Consultant "Our great and glorious masterpiece is to live appropriately" -- Michel de Montaigne (1533-1592) *************************************************************************** From chemistry-request@www.ccl.net Fri Feb 5 13:46:01 1999 Received: from mail.wesleyan.edu (mail.wesleyan.edu [129.133.1.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA06716 Fri, 5 Feb 1999 13:46:00 -0500 (EST) Received: from sunfish (sunfish.chem.wesleyan.edu [129.133.20.34]) by mail.wesleyan.edu (8.9.1/8.9.1) with SMTP id NAA15673 for ; Fri, 5 Feb 1999 13:46:03 -0500 (EST) Message-Id: <3.0.5.32.19990205134705.012685c0@wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Fri, 05 Feb 1999 13:47:05 -0500 To: chemistry@www.ccl.net From: Yongxing Liu Subject: Metal ion-water complex calculations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers, Would any one please point to me any references of ab initio, semiempirical, DFT calculations on metal ion-water complexes? The metal ions I am interested in are Na+, K+, Mg2+, Zn2+, Cl-, etc. Thanks a lot in advance. Sincerely, Yongxing Liu From chemistry-request@www.ccl.net Fri Feb 5 14:20:06 1999 Received: from aims.pdl.com (aims.pdl.com [198.93.156.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA10230 Fri, 5 Feb 1999 14:20:04 -0500 (EST) Received: from nastagate (198.93.157.7) by aims.pdl.com with SMTP (Eudora Internet Mail Server 1.3.1); Fri, 5 Feb 1999 11:18:38 -0800 From: MVasquez@pdl.com (Max Vasquez) To: CHEMISTRY@www.ccl.net Date: Fri, 5 Feb 1999 10:17:18 -0800 Subject: Re: CCL:Histogram method, redux (fwd) Message-ID: References: Organization: Protein Design Labs, Inc. MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Content-ID: X-Gateway: NASTA Gate 2.0 for FirstClass(R) stewart@uga.edu writes: >Here are some references to early papers describing the multicanonical >method: > B. Berg and T. Neuhaus, Phys. Lett. B267, 249 (1991). > B. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992). > B. Berg, U. Hansmann and T. Neuhaus, Z. Phys. B90, 229 (1993). > W. Janke, B. Berg and M. Katoot, Nucl. Phys. B382, 649 (1992). >There have been more recent papers, but these should be enough to give >you >a feel for the method and decide if it will meets your needs. Hansmann has applied the multicanonical method to study folding of atomistic models of relatively short peptides; see J. Phys. Chem. B 102, 653-656 (1998) for a recent reference, and J. Comp. Chem. 14, 1333-1338 (1993) for one of the first (if not *the* first) applications of multicanonical methods to protein/peptide folding. The work of Hao and Scheraga with lattice models of proteins is also worth checking (note that they call the procedure "entropy sampling", but this is equivalent to multicanonical); see for example, J. Phys. Chem. 98, 4940-4948 (1994). *********************************** Max Vasquez Protein Design Labs, Inc. (510) 574-1477 (510) 574 1500 (FAX) From chemistry-request@www.ccl.net Fri Feb 5 20:19:05 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA01685 Fri, 5 Feb 1999 20:19:05 -0500 (EST) Received: from mail1.its.rpi.edu (root@mail1.its.rpi.edu [128.113.100.7]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id UAA20644 for ; Fri, 5 Feb 1999 20:19:03 -0500 (EST) Received: from brenemanP2.chem.rpi.edu (rts16p3.xyp.rpi.edu [128.113.30.132]) by mail1.its.rpi.edu (8.8.8/8.8.6) with SMTP id UAA30194 for ; Fri, 5 Feb 1999 20:20:38 -0500 Message-ID: <36BB98A1.61AC@rpi.edu> Date: Fri, 05 Feb 1999 20:19:29 -0500 From: "Prof. Curt M. Breneman" Organization: Rensselaer Polytechnic Institute X-Mailer: Mozilla 3.04 (Win95; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Electric Fields in Gaussian94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Folks, I am interested in applying uniform electric fields to the hamiltonian within Gaussian94 for the purpose of generating finite-difference polarizabilies. It seems to me that there is a way to apply such fields within Gaussian, but I can't seem to find it. Can anyone help? Curt Breneman RPI Chemistry From chemistry-request@www.ccl.net Fri Feb 5 21:24:23 1999 Received: from ce.ifisicam.unam.mx (ce.fis.unam.mx [132.248.33.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA01870 Fri, 5 Feb 1999 21:24:22 -0500 (EST) Message-Id: <199902060224.VAA01870@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.4/16.2) id AA04012; Fri, 5 Feb 1999 20:15:00 -0600 From: Ramon Garduno Subject: Seeking NAOMI software.... To: CHEMISTRY@www.ccl.net (CCL POST MSG) Date: Fri, 5 Feb 99 20:14:59 CST Mailer: Elm [revision: 70.85] Dear CCLers: I have used most of the Web search engines to get in touch with Prof. Simon M. Brocklehurst, author of NAOMI, without success. My query is in order to obtain the most recent version (2.4c) of this software but apparently he has moved from smb@bioch.ox.ac.uk to how knows where. Does any of you have information leading to the appropiate email or URL address?. Much obliged, Ramon Garduno -- "...De los 260 musculos que tiene el cuerpo humano, el mas dificil de mantener en forma es el corazon...." ___________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics CENTRO DE CIENCIAS FISICAS | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | Apdo. 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