From chemistry-request@server.ccl.net Fri Jan 26 21:33:35 2001 Received: from pn2.vsnl.net.in (pn2.vsnl.net.in [202.54.10.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0R2XXw21165 for ; Fri, 26 Jan 2001 21:33:34 -0500 Received: from pn2.vsnl.net.in ([203.199.128.157]) by pn2.vsnl.net.in (8.9.0/8.9.0) with ESMTP id HAA16989; Sat, 27 Jan 2001 07:59:27 +0530 (IST) Message-ID: <3A723780.CF686560@pn2.vsnl.net.in> Date: Sat, 27 Jan 2001 08:20:40 +0530 From: "Dr. Gadres" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: tcg@chem.unipune.ernet.in, Renxiao Wang , CHEMISTRY@server.ccl.net Subject: Re: CCL:Solvate organic molecules?ANANT ANANT ANANT References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Wang : We have developed a model, named as EPIC, for this purpose. You may look up our papers in J.Phys. Chem. and Ind. J. Chem. in 1998-2000 for this purpose. Currently we are extending it for larger number of water molecules. Of course, what contitutes the "first layer" or "first shell" is rather difficult to define. We have been able to use EPIC structure for ab initio studies. The agreement for energies is reasobaly good. For example, we have studied thyamine..n H2O with n upto 20, formaimide with upto 20 etc. Please contact us for details if interested. Thanks...Shridhar Gadre > On Thu, 25 Jan 2001, Renxiao Wang wrote: > > >For some reasons we need to solvate organic molecules or even proteins > >with explicit water molecules. Will anybody recommend a reliable algorithm > >for doing this? It will be ideal if it is able to reproduce the 'real' > >situations. The first layer of water is enough. > > > >Please note that we prefer an algorithm rather than a certain program. It > >is simply because we are writing programs in our approach. We certainly > >know about some programs, such as AMBER and CHARMm, which can place waters > >around a given molecule. But we are a little bit skeptical for what they > >generate on the screen. > If this makes you skeptical, then try quantum mechanics or X-ray > crystallography instead. Writing a program in "your own approach" will > certainly not improve the result unless you use a better description > than molecular mechanics (i.e. quantum chemistry). > > Groeten, David. > ________________________________________________________________________ > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > phone: 46 18 471 4205 fax: 46 18 511 755 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > -= 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 Jan 27 04:41:51 2001 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0R9fow22990 for ; Sat, 27 Jan 2001 04:41:50 -0500 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Sat, 27 Jan 2001 10:43:09 +0100 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA10061; Sat, 27 Jan 2001 10:41:48 +0100 Date: Sat, 27 Jan 2001 10:41:48 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: Adam Hixson Cc: CHEMISTRY@ccl.net Subject: Re: CCL:SHAKE and the MCE. In-Reply-To: <20010126214042.21344.qmail@web1106.mail.yahoo.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 26 Jan 2001, Adam Hixson wrote: >I just read one of the original accounts of the >SHAKE algorythm (J Comp Phys 1977 23 327-41), >and I have a question about the energy produced. > >To what extent does a microcannonical ensemble >simulation using SHAKE conserve the energy? The >authors of the above paper mentioned that it >fluxuated about a stable value, but gave no >indication as to how great the flux was. > >Anybody know anything about this? Energy conservation is very good, but probably not quite as good as when using normal potentials like harmonic bonds etc. because you still have to use a numerical solution for the constraint equations. You can usually set a tolerance that determines how good the convergence should be, but lower tolerance means higher computational cost. It is worth mentioning that there is also a "follow up" algorithm to shake that is non iterative: @article{Hess97, author = {B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije}, title = {{LINCS}: A Linear Constraint Solver for Molecular Simulations}, journal = "J. Comp. CHem.", year = 1997, volume = 18, pages = {1463--1472} } Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Sat Jan 27 16:38:20 2001 Received: from tomts7-srv.bellnexxia.net (tomts7.bellnexxia.net [209.226.175.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0RLcKw27050 for ; Sat, 27 Jan 2001 16:38:20 -0500 Received: from HSE-Montreal-ppp103712.qc.sympatico.ca ([64.230.178.25]) by tomts7-srv.bellnexxia.net (InterMail vM.4.01.03.00 201-229-121) with ESMTP id <20010127213620.HPJY6682.tomts7-srv.bellnexxia.net@HSE-Montreal-ppp103712.qc.sympatico.ca> for ; Sat, 27 Jan 2001 16:36:20 -0500 Date: Sat, 27 Jan 2001 16:39:12 -0500 From: "Qadir K. Timergazin" X-Mailer: The Bat! (v1.46) Reply-To: "Qadir K. Timergazin" Organization: Universite Concordia X-Priority: 3 (Normal) Message-ID: <9476598165.20010127163912@alcor.concordia.ca> To: chemistry@ccl.net Subject: Linux 2.4.0 and 2 GB promlem Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I've heard that new Linux kernel 2.4.0 can handle files larger than 2 GB. Have anybody tried to test 2.4.0 kernel with quantum-chemical programs? -- Best regards, Qadir Timerghazin mailto:q_timerg@alcor.concordia.ca