From chemistry-request@server.ccl.net Fri Jun 16 11:19:11 2000 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06891 for ; Fri, 16 Jun 2000 11:19:11 -0400 Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA112098345; Fri, 16 Jun 2000 11:12:25 -0400 Date: Fri, 16 Jun 2000 11:12:25 -0400 (EDT) From: Rick Venable To: Marcos Villarreal Cc: chemistry@ccl.net Subject: Re: CCL:decane In-Reply-To: <00061519182400.01043@fer-net.fcq.unc.edu.ar> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It's not so hard to make one. o run Langevin or Monte Carlo on a single decane o randomly sample saved coords and place them on an oversized grid o apply periodic bondary conditions, and run some const P dynamics If you allow a little extra space between molecules and then use const P to adjust your box size, it is fairly straightforward and trouble free. I just did this to make an octane box myself using CHARMM. On Thu, 15 Jun 2000, Marcos Villarreal wrote: > were could I find an equilibrated box of decane (all or united > atom) to perform a molecular dynamics? -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov )