From chemistry-request@ccl.net Thu Apr 1 23:35:06 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i324Z4js012518 for ; Thu, 1 Apr 2004 23:35:05 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i324cSeO019794 for ; Thu, 1 Apr 2004 23:38:29 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i324cQRX019782; Thu, 1 Apr 2004 23:38:26 -0500 Date: Thu, 1 Apr 2004 23:37:25 -0500 From: Rick Venable To: martin$at$yangtze.hku.hk cc: chemistry$at$ccl.net Subject: CHARMM dummy atoms In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable$at$nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 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 An aside: those with CHARMM related questions may wish to try the web based bulletin board system at www.charmm.org A number of developers and advanced users participate regularly. On Thu, 1 Apr 2004 martin$at$yangtze.hku.hk wrote: > I would like to consult about how to add two or more dummy atoms in > Charmm? Dummy atoms are used for a variety of purpose, and can be assigned arbitrary properties by editing RTF and PARAM files if needed. It really depends on how you want to use these dummy atoms. There is an existing DUM atom type in several of the distributed RTF/PARAM file pairs. > Actually, I am calculating a system with 2 segments. I would like > to introduce constant velocity to 1 segment (all the atoms in segment > move in one direction with same spped). > > How can I do so? Modify the velocities in a dynamics restart file; they are listed for each atom in PSF order, which is the same ordering as that in the corresponding CHARMM .crd file. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable$at$nih.gov ALT email: rvenable$at$speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=