From chemistry-request@server.ccl.net Sun Aug 27 09:53:04 2000 Received: from fjohn.Stanford.EDU (fjohn.Stanford.EDU [171.64.38.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA06254 for ; Sun, 27 Aug 2000 09:53:04 -0400 Received: from localhost (greg@localhost) by fjohn.Stanford.EDU (8.9.3/8.9.3) with ESMTP id GAA26111 for ; Sun, 27 Aug 2000 06:52:51 -0700 Date: Sun, 27 Aug 2000 06:52:51 -0700 (PDT) From: Greg Lakatos To: chemistry@ccl.net Subject: Normal mode generation with CHARMm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Recently I've started using CHARMm to calculate the normal modes of a moderately sized macromolecule (1254 atoms), and have run into some difficulty. 1) CHARMm only generates 3 modes with a 0 frequency whereas I was expecting 6 modes with 0 frequency (3 rigid body translations, 3 rigid body rotations) 2) CHARMm generates negative frequencies corresponding to negative eigenvalues. If CHARMm is diagonalizing the matrix corresponding to the linearized equations of motion, then shouldn't a negative eigenvalue give a complex frequency (Non-oscillatory behavior)? In any event, why generate negative frequencies? The normal modes were calculated with the molecule in its minimum energy configuration through the use of the DIAG command. Any help would be greatly appreciated. Thanks, Greg Lakatos (greg@fjohn.stanford.edu) From chemistry-request@server.ccl.net Sun Aug 27 14:52:19 2000 Received: from mail2.zrz.tu-berlin.de (mail2.zrz.TU-Berlin.DE [130.149.4.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA07272 for ; Sun, 27 Aug 2000 14:52:18 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.16) id 13T7XW-0007fQ-00; Sun, 27 Aug 2000 20:52:18 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.16) id 13T7XV-0005MM-00; Sun, 27 Aug 2000 20:52:17 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: References: Date: Sun, 27 Aug 2000 20:52:20 +0200 To: Greg Lakatos From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:Normal mode generation with CHARMm Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" >1) CHARMm only generates 3 modes with a 0 frequency whereas I was >expecting 6 modes with 0 frequency (3 rigid body translations, 3 rigid >body rotations) you cannot expect zero frequency for the "linearized" rotational modes unless you are *exactly* at a stationary point. The "true" rotations of course can only be expressed in curvilinear coordinates, the linearized ones will also stretch the bonds. -- +---------------------------------+------------------------------------+ | Prof. Christoph van Wullen | Tele-Fon (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail: | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.DE | +---------------------------------+------------------------------------+