From chemistry-request@ccl.net Fri Apr 23 17:19:04 2004 Received: from scn4.scn.org (scn4.scn.org [66.212.64.197]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3NMJ2KC004461 for ; Fri, 23 Apr 2004 17:19:03 -0500 Received: from scn.org (er-chan@scn [66.212.64.194]) by scn4.scn.org (8.9.1-20031009/8.9.1) with ESMTP id PAA18555; Fri, 23 Apr 2004 15:11:49 -0700 (PDT) Received: from localhost (er-chan@localhost) by scn.org (8.9.1-20031009/8.9.1) with ESMTP id PAA23600; Fri, 23 Apr 2004 15:20:14 -0700 (PDT) Date: Fri, 23 Apr 2004 15:19:54 -0700 (PDT) From: er-chan To: Masakatsu Ito cc: chemistry)at(ccl.net Subject: Re: CCL:Jarzynski's equality for free energy In-Reply-To: <20040422.141916.468716365.Masakatsu Ito)at(ccg.flab.fujitsu.co.jp> Message-ID: 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 Hello Computational Chemistry List (On 04/22/04,2:19pm,you wrote Re:... arXiv:cond-mat/0404475 MI> Hi CCLers, MI> MI> I am looking for reviews and articles about the free energy MI> calculation of biomolecules. I have been impressed by Jarzynski's MI> equality (Phys.Rev.Lett. 78, 2690 (1997)) which enables one to MI> estimate free energy difference from an ensemble of short MD MI> simulations. This implies that the estimation can be drastically MI> accelerated by distributed computing. But those MD simulations should MI> start from equilibrium, and I am wondering how such initial conditions MI> can be prepared for biomolecules. Because it is notoriously difficult MI> to get an equilibrium ensemble of biomolecular structures. MI> MI> Thus I am very interested in the application of Jarzynski's equality MI> to biomolecular processes. Could someone please give me some advice or MI> point me to articles? MI> MI> Thanks in advance for any help. MI> Kind Regards, MI> MI> Masakatsu Ito , Ph.D MI> MI> Nanotechnology Research Center MI> FUJITSU LABORATORIES LTD. MI> 10-1 Morinosato-Wakamiya, Atsugi 243-0197 Japan MI> Phone : +81-46-250-8234 Fax : +81-46-250-8844 MI> E-mail m-ito)at(jp.fujitsu.com MI> MI> MI> -= This is automatically added to each message by the mailing script =- MI> To send e-mail to subscribers of CCL put the string CCL: on your Subject: line MI> and send your message to: CHEMISTRY)at(ccl.net MI> MI> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net MI> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs MI> MI> If your mail is bouncing from CCL.NET domain send it to the maintainer: MI> Jan Labanowski, jlabanow)at(nd.edu (read about it on CCL Home Page) MI> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ MI> MI> MI> MI> MI> MI> From chemistry-request@ccl.net Sat Apr 24 16:23:07 2004 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3OLN5KC026653 for ; Sat, 24 Apr 2004 16:23:06 -0500 Received: from 192.168.0.101 (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i3OLO9T9023186 for ; Sat, 24 Apr 2004 14:24:10 -0700 Date: Sat, 24 Apr 2004 14:24:05 -0700 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <1391216937.20040424142405(at)joyie.com> To: chemistry(at)ccl.net Subject: The dispersion forces in B3LYP calcualtion in G03 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=2.0 required=7.5 tests=DNS_FROM_RFCI_DSN, FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLers, In the calculation of water clusters. The binding energy calculated by DFT hybrid model is smaller than that did by MP2 method. This could be due to the miss of dispersion forces in the model. I wonder in G03 does this forces have been added to the DFT hybrid model? -- Best regards, John Lee