From owner-chemistry@ccl.net Wed May 3 03:38:00 2006 From: "Sigismondo Boschi s.boschi|*|cineca.it" To: CCL Subject: CCL:G: Cartesian Coordinate Transformation Message-Id: <-31676-060503033611-26915-Zbt/rYkIoXpbperNZJy7bQ{:}server.ccl.net> X-Original-From: Sigismondo Boschi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 3 May 2006 09:35:55 +0200 (MEST) MIME-Version: 1.0 Sent to CCL by: Sigismondo Boschi [s.boschi()cineca.it] Xiaobo Zheng xiaoboccl:+:gmail.com wrote: > Sent to CCL by: "Xiaobo Zheng" [xiaoboccl#%#gmail.com] > Dear CCLer, > > I am using Gaussian to optimized geometries with constraints and my input format is in cartesian coordinate. But after optimization, somtimes, Gaussian output does not contain my original cartesian coordinate information. Instead, it reports "standard orientation", which is a transformation of my original coordinate. I am just wondering if there is an easy way or tools to transform Gaussian "starndard orientation" back to my cartesian coordinate. Hi, I was playing with rotations just in these days... I would do it in this way: - get the inertia tensor I of the original molecule - find the corresponding rotation matrix R that rotate it in its standard orientation, by finding the eigenvalues of I. - apply the inverse of R to the last molecules got from gaussian. The two molecules now should come in a "similar" orientation... you can not state that they are in the same, since the two molecules are different. Just their inertia tensor are in the same orientation. Otherwise, if you want to let the two molecules have a particular group aligned, like a phenyl, you need to play differently with rotations/translations. I hope this helps. Regard, Sigismondo -- ------------------------------------------------------------------------------- User Guide: http://www.cineca.it/sap/files/user_guide_cineca.pdf SUPPORT REQUESTS: superc:cineca.it ** PERSONAL ADDRESS: s.boschi:cineca.it ** ------------------------------------------------------------------------------- Sigismondo Boschi, Ph.D. tel: +39 051 6171559 CINECA (High Performance Systems) fax: +39 051 6137273 - 6132198 via Magnanelli, 6/3 http://instm.cineca.it 40033 Casalecchio di Reno (BO)-ITALY http://www.cineca.it