From chemistry-request@ccl.net Sun Aug 31 12:31:29 2003 Received: from GWIA.HSC.WVU.EDU (gateway.hsc.wvu.edu [157.182.105.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7VGVTvj001712 for ; Sun, 31 Aug 2003 12:31:29 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Sun, 31 Aug 2003 12:31:36 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.3 Date: Sun, 31 Aug 2003 12:31:38 -0400 From: "Peter Gannett" To: , Subject: Re: CCL:can someone identify this molecule? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h7VGVTvj001713 Roma: Given the amount of worms, virii, etc attached to email these days, I'm not sure I'm inclinded to open the attachment. Perhaps you could give the link to where it was downloaded from. Pete >>> "Roma Oakes" 08/30/03 22:41 PM >>> Hi all Some time ago I downloaded this picture to use in a talk - of course I assumed that I would remember exactly what it was (and I did at the time). Now I want to use it again but cannot remember its name. I know I should have written it all down - I have already kicked myself!! Please help Roma From chemistry-request@ccl.net Sun Aug 31 20:38:50 2003 Received: from lac.chem.nagoya-u.ac.jp (lac.chem.nagoya-u.ac.jp [133.6.84.199]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h810cnvj009261 for ; Sun, 31 Aug 2003 20:38:50 -0400 Received: from lac2.chem.nagoya-u.ac.jp (lac2.chem.nagoya-u.ac.jp [133.6.84.36]) by lac.chem.nagoya-u.ac.jp (Postfix) with ESMTP id 9547BD9DC4 for ; Mon, 1 Sep 2003 09:38:48 +0900 (JST) From: Hannes Loeffler Organization: University of Nagoya To: chemistry|at|ccl.net Subject: Re: CCL:error message from CHARMM: too many IM contacts? Date: Mon, 1 Sep 2003 09:40:25 +0900 User-Agent: KMail/1.5 References: <200308200929.58597.HLoeffler|at|lac.chem.nagoya-u.ac.jp> In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset="shift_jis" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200309010940.25341.HLoeffler|at|lac.chem.nagoya-u.ac.jp> On Thursday 21 August 2003 05:11, you wrote: > On Wed, 20 Aug 2003, Hannes Loeffler wrote: > > what does this error message mean and how can I avoid it? > > > > ***** LEVEL -4 WARNING FROM ***** > > ***** GENERATING TOO MANY IM CONTACTS > > The message suggests that some of your nonbond and image choices, esp. > cutoffs, may be requiring too much memory. It's difficult to tell w/o > seeing some more of the output. Some things to try: > > [1] reduce CUTIM; it can be the same size as CUTNB (but not smaller) > > [2] use a CHARMM executable with a larger atom limit > > Another possibility is that the machine type you're using doesn't > support dynamic expansion of the HEAP data structure; this has been a > problem on some 64-bit architectures in the past. I'm not sure of the > current status of this problem. Thank, you very much for your suggestions. Unfortunately the problems still remains (CUTIM reduced, large, xxlarge). The only "solution" I found was to set BOMLEV to -5, though I don't know it's implications. I have no idea which output could be more helpful as the output of a failed run looks pretty much the same as in a successful run. The computer system is Linux running on a Pentium IV. The simulation system is just a single ion immersed in 499 TIP3P. Many thanks for your help, Hannes.