From chemistry-request@ccl.net Fri Jul 9 15:03:33 2004 Received: from mx5.net.nih.gov (mx5.net.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69K3WUW012691 for ; Fri, 9 Jul 2004 15:03:32 -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 i69K9NMK000752 for ; Fri, 9 Jul 2004 16:09:23 -0400 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 i69K9N61000711; Fri, 9 Jul 2004 16:09:23 -0400 Date: Fri, 9 Jul 2004 16:06:48 -0400 From: Rick Venable To: h9807907=at=hkusua.hku.hk cc: CHEMISTRY=at=ccl.net Subject: Re: CCL:Questions about CHARMM I/O In-Reply-To: <1089366908.40ee6b7c24f87=at=imp.webmail.hku.hk> Message-ID: References: <1089366908.40ee6b7c24f87=at=imp.webmail.hku.hk> ReplyTo: Rick_Venable=at=nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Reminder: try the CHARMM Forums at www.charmm.org for questions about using academic CHARMM. (Questions about using the commercial CHARMm product via Quanta or InSight should be directed to Accelrys). On Fri, 9 Jul 2004 h9807907=at=hkusua.hku.hk wrote: > I am new to CHARMM and I hope that you can give me some ideas of the following > questions. > 1) Do anyone know how to print out the coordinate file and restart file at > different time intervals during a MD similation? Is that possible by modifying > the .inp file? The coordinates are saved in the trajectory file indicated by IUNCRD every NSAVC integration steps; change NSAVC to change the frequency for saving coordinate sets. By default, the restart file is only written once, at the end of the run; for modern computer systems with low failure rates, this is the preferred method. The ISVFRQ option of DYNAmics can be used to write the restart file (to the unit specified by IUNWRI) more often. > 2) How can I suppress the print of those files, such as .vel .ene, which I > cannot read? Don't open the files and assign unit numbers, and don't specify a frequency (in integration steps) for these, i.e. the DYNAmics command would include IUNVEL -1 NSAVV 0 KUNIT -1 The .ene file should be readable, just not easily understood. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=