From chemistry-request@ccl.net Fri Oct 24 10:10:53 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9OEAJMV024068 for ; Fri, 24 Oct 2003 10:10:19 -0400 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id h9OEAImc014681 for ; Fri, 24 Oct 2003 11:10:18 -0300 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id h9OEAHkg020582 for ; Fri, 24 Oct 2003 11:10:17 -0300 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id h9OEAHrJ020580 for chemistry~at~ccl.net; Fri, 24 Oct 2003 11:10:17 -0300 Received: from athlon2.chem.unb.ca (athlon2.chem.unb.ca [131.202.171.176]) by webmail.unb.ca (IMP) with HTTP for ; Fri, 24 Oct 2003 11:10:17 -0300 Message-ID: <1067004617.3f9932c9668c8~at~webmail.unb.ca> Date: Fri, 24 Oct 2003 11:10:17 -0300 From: Joey Harriman To: CCL posting Subject: Implicit MD simulations in AMBER MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.171.176 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-0.6, required 5, SPAM_PHRASE_02_03, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-0.3 required=7.0 tests=USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi everyone, I am currently in the process of running some implicit MD simulations in Amber7. As far as I can tell the only flags that need to be included in the MD input file are: gbsa=1 igb=1 extdiel=*** Can anyone confirm this? In addition, I am trying to do a MD simulation on a ligand in Toluene (extdiel=2.4)...are there any suggestions to make this calculation faster? I am currently usine SHAKE 2 for the calculations. Thanks in advance for your response, Joey Harriman ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o~at~unb.ca 476-6543 ----------------------------------