Received: from mail.netbsd.org (mail.netbsd.org [204.152.190.11]) by www.NetBSD.org (Postfix) with ESMTP id B427963B84C for ; Sat, 14 Jan 2012 00:38:22 +0000 (UTC) Received: by mail.netbsd.org (Postfix, from userid 605) id 5BEFA14A270; Sat, 14 Jan 2012 00:38:22 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 2639014A267 for ; Sat, 14 Jan 2012 00:38:19 +0000 (UTC) X-Virus-Scanned: amavisd-new at NetBSD.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.NetBSD.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id Rwqv00IFgHTR for ; Sat, 14 Jan 2012 00:38:18 +0000 (UTC) Received: from cvs.netbsd.org (cvs.NetBSD.org [IPv6:2001:4f8:3:7:2e0:81ff:fe30:95bd]) by mail.netbsd.org (Postfix) with ESMTP id 98E8F14A266 for ; Sat, 14 Jan 2012 00:38:18 +0000 (UTC) Received: by cvs.netbsd.org (Postfix, from userid 500) id 731D0175DD; Sat, 14 Jan 2012 00:38:18 +0000 (UTC) MIME-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Sat, 14 Jan 2012 00:38:18 +0000 From: "Aleksej Saushev" Subject: CVS commit: pkgsrc/biology/gromacs To: pkgsrc-changes@NetBSD.org Reply-To: asau@netbsd.org X-Mailer: log_accum Message-Id: <20120114003818.731D0175DD@cvs.netbsd.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk Module Name: pkgsrc Committed By: asau Date: Sat Jan 14 00:38:18 UTC 2012 Modified Files: pkgsrc/biology/gromacs: Makefile PLIST distinfo Log Message: Update to Gromacs 4.5.5 Notable changes in Gromacs 4.5.5: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending truncating files to 0 bytes when continuation runs stopped before writing new output. * Fixed COM pulling with multiple constraints checking the convergence of one constraint instead of all. * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms. * AmberGS force field is now based on Amber94 instead of Amber96. * Moved hydrogens in Charmm27 protein termini to separate charge groups and added ACE and CT3 residue types. * Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. * Many small updates to the manual pages of programs. To generate a diff of this commit: cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/gromacs/Makefile cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/gromacs/PLIST cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/gromacs/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files.