From chemistry-request@ccl.net Tue May 4 11:08:10 2004 Received: from mail.scs.uiuc.edu (mail.scs.uiuc.edu [130.126.231.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44G89kh008821 for ; Tue, 4 May 2004 11:08:10 -0500 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by mail.scs.uiuc.edu with esmtp; Tue, 04 May 2004 11:09:52 -0500 Reply-To: jerome~at~scs.uiuc.edu From: "Jerome Baudry" To: "'Ravindra VenKatramani'" Cc: chemistry~at~ccl.net Subject: RE: Rigid body simulations in charmm Date: Tue, 4 May 2004 11:07:33 -0500 Message-ID: <004401c431f1$e9339e10$efe27e82@leonidas> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 In-Reply-To: <080F78D8-9DB2-11D8-B1F4-000A95999556~at~cnrs-orleans.fr> Importance: Normal 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 What about fixing all internal coordinates in the to-be-rigid-molecule: using the CONS ICcommand ? all bonds must have the same restraint constant (same for angles, dihedrals etc..) , but since you want to define a rigid body, you can use one unique very high constant. You would have to define explicitly all ICs in the CONS IC command, but doable since you're dealing with a dipeptide.. ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome~at~scs.uiuc.edu > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request~at~ccl.net]On > Behalf Of Konrad Hinsen > Sent: Tuesday, May 04, 2004 5:02 AM > To: Ravindra VenKatramani > Cc: chemistry~at~ccl.net > Subject: CCL:Rigid body simulations in charmm > > > On May 3, 2004, at 7:02, Ravindra VenKatramani wrote: > > > My first thought is to define the dipeptide structure only > > thorugh > > bonds (no angles or dihederals) and use SHAKE to keep the peptide > > fixed. > > Doing so i`m running into SHAKE convergence problems during > the heating > > and equilibration stage. Am i missing something in this > simple minded > > approach? Is there an alternate way to perform rigid body > simulations? > >>