From chemistry-request#* at *#server.ccl.net Tue May 13 03:53:37 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4D7rbt11678 for ; Tue, 13 May 2003 03:53:37 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h4D7raru075365 for ; Tue, 13 May 2003 09:53:36 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h4D7rarj339035; Tue, 13 May 2003 09:53:36 +0200 (MEST) Date: Tue, 13 May 2003 09:53:36 +0200 (MEST) From: Michel Petitjean Message-Id: <200305130753.h4D7rarj339035 $#at#$ ds10.itodys.jussieu.fr> To: chemistry.,at,.ccl.net Subject: CCL:Re: How to calculate molecular volume X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CCL Subject: CCL:Re: How to calculate molecular volume The ASV freeware computes analytically surfaces and volumes of any union of spheres. The precision is near the machine real*8 precision, and thus the volumes values may be used for numerical calculations of gradients. The reliability is good, since the method handles all topological situations for the set of spheres, including those which are never encountered in chemistry. If your input set contains some uncertainty, you can automatically generate perturbated inputs and see the effects on the analytical values. If you need real*16 precision, I can recompile for you the f77 source, provided that this is on a platform enabling it (e.g. the IBM autodblpad compiler option). The freeaware ASV includes also a Monte-Carlo calculation of surfaces and volumes (with precision calculus), which is useful if you need a short computing time for large sets, and provided that a limited precision suffice, such as for empirical correlations. See programmes, documentation, and ref. of the method on: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV The rectangular grid containing the molecule may be approximated > from the xmin,xmax, ymin,ymax, zmin,zmax via random rotations. Before doing that, since the parallelepiped box is convex, you can first extract the extremal points which the RADI freeware, which computes also the minimal sphere containing your set of points. See programmes, documentation and reference on: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean.,at,.itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean |-at-| ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html =?gb2312?q?Jinsong=20Zhao?= wrote: >Dear all, > >I hope to know if there is any program or routine >could calculate the molecular volume with high >precision and reliability, moreover, to figure out the >length, width and high of the grid that contain the >molecule.=20 > >Any comments, suggestion are welcome! > >Thanks for essential responses! > >Best regards, > >Jinsong