From chemistry-request@server.ccl.net Thu Aug 2 23:07:03 2001 Received: from tomts14-srv.bellnexxia.net ([209.226.175.35]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f73373v13300 for ; Thu, 2 Aug 2001 23:07:03 -0400 Received: from test ([64.229.239.89]) by tomts14-srv.bellnexxia.net (InterMail vM.4.01.03.16 201-229-121-116-20010115) with SMTP id <20010803035515.YUNU20283.tomts14-srv.bellnexxia.net@test> for ; Thu, 2 Aug 2001 23:55:15 -0400 Message-ID: <003801c11bcf$ff8e9880$c66efea9@test> From: =?iso-8859-1?Q?Jonathan_Despr=E9s?= To: Subject: NanotechNews.com, a website delivering news. Date: Thu, 2 Aug 2001 23:54:29 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hi Guys, Just a quick note, you can read ALOT of news on nanotechnology here: http://www.nanotechnews.com It's very good, we post news on nanotech in mass, 3 or 4 news per day, which is big. Our competitors don't surpass us. It's all free, so enjoy and learn! --Jon From chemistry-request@server.ccl.net Fri Aug 3 12:43:27 2001 Received: from Salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f73GhQv15188 for ; Fri, 3 Aug 2001 12:43:27 -0400 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.0-24 #36961) id <0GHI00L013S6TS@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Fri, 03 Aug 2001 17:43:20 +0100 (BST) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.0-24 #36961) with ESMTP id <0GHI00J0X3S6WF@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Fri, 03 Aug 2001 17:43:18 +0100 (BST) Date: Fri, 03 Aug 2001 17:43:17 +0100 From: Laurence Cuffe Subject: g98 and jaguar/HP workstations/Itanium To: CHEMISTRY@ccl.net Message-id: <3B6AE2B5.26512.F6A64@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal We are considering a new HP workstation for running G98 and jaguar jobs. The systems were looking at are the HP i2000 with the Itanium 800 Mhz processors and the HP9000 A500 with two PA-8500 or PA 8600 processors. We would appreciate any feedback from anyone who has run either program on either platform. A particular concern is whether g98 will run on the Itanium processor. HP say "Of course, all your current PA-RISC binaries will run on Itanium." But what this means in practice is an open question. Also if anyone has any other suggestions as to hardware platforms these would be most welcome. All the best Laurence Cuffe If requested I will summarize; From chemistry-request@server.ccl.net Fri Aug 3 12:10:45 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f73GAjv14235 for ; Fri, 3 Aug 2001 12:10:45 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA24284; Fri, 3 Aug 2001 12:10:42 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3B6AC7A0.3FBADF82@cornell.edu> Date: Fri, 03 Aug 2001 11:47:44 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: A rather strange situation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Even though I my Ph. D. thesis work was doing molecular dynamics simulations, I don't claim to be an expert in the field. That being said, I have still never seen the following situation which I will describe to you. Any input or suggestions will be most welcome and appreciated. I have been doing MD simulations using CHARMM on a small peptide having 27 amino acid residues, both in vacuum and in solution. I have also done some simulations where the peptide is heavily glycosylated, again both in solution and in vacuum. Originally, the sugars were alpha-linked, but now I have linked them beta. The redone vacuum calculation is ok, but the solvated system is giving me problems. By that I mean, when I run the dynamics, I get nans (not a known quantity, basically) where I would normally get a value. Yet, what I find is strange is that the calculation runs, and if you look at the trajectory (i.e., run a "movie") everything seems to look ok. I've tried everything I can think of, including trying to minimize the heck out of the system. Everything else is the same except the sugars are beta. My theory (I know, bad word...lol) is that it has something to do with the conformation of the peptide and the fact that it has all these sugars. Initially, I had half of the peptide in an alpha-helical like conformation (because this was a project that someone else had started to work on, and I picked up where they left off), and I think that the the part that was helical (which has 4 threonine residues, btw, which have 9 sugars attached) allowed the sugars to interact LESS than they are now. This increased sugar-sugar interaction (?) is somehow driving the energy of the system in water through the roof so to speak. At least, that is my theory. Does anyone have any experience with situations like this and have a way to work around it? Any additional suggestions are also welcome. Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Fri Aug 3 13:08:40 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f73H8ev17716 for ; Fri, 3 Aug 2001 13:08:40 -0400 Received: from demetrio.u.arizona.edu (128.196.86.129) by deimos.email.Arizona.EDU (5.1.056) id 3B5F1B9D000B2C65 for CHEMISTRY@ccl.net; Fri, 3 Aug 2001 10:08:38 -0700 Message-Id: <5.1.0.14.0.20010803095350.03ecba40@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 03 Aug 2001 10:07:26 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: Molecular Dynamics Simulations In-Reply-To: <003801c11bcf$ff8e9880$c66efea9@test> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_60599157==_.ALT" --=====================_60599157==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I want to find software that can be used in molecular dynamic simulations of organic molecules and polymers containing aromatic groups. It would be really nice if this software lets me introduce the developments that several groups are doing on that field. For example, I have an article in my hands by Smith et al (G. D. Smith and R. L. Jaffe, J. Phys. Chem. 1996, 100, 9629-9630) where I find force field parameters for Benzene and I would like to have the possibility to introduce those parameters in such a software in order to simulate a benzene crystal. Thanks for your help and I will sumarize the answers. Demetrio Filho --=====================_60599157==_.ALT Content-Type: text/html; charset="us-ascii" Dear CCL'ers,

I want to find  software that can be used in molecular dynamic simulations of organic molecules and polymers containing aromatic groups.

It would be really nice if this software lets me introduce the developments that several
groups are doing on that field.   For example, I have an article in my hands by Smith et al (G. D. Smith and R. L. Jaffe, J. Phys. Chem. 1996, 100, 9629-9630) where I find  force field parameters for Benzene and I would like to
have the possibility to introduce those parameters in such a software in order to simulate a benzene crystal.

Thanks for your help and I will sumarize the answers.

Demetrio Filho


 --=====================_60599157==_.ALT-- From chemistry-request@server.ccl.net Fri Aug 3 16:10:41 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f73KAfv27473 for ; Fri, 3 Aug 2001 16:10:41 -0400 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id f73KAeH18377; Fri, 3 Aug 2001 15:10:40 -0500 (CDT) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id PAA21556; Fri, 3 Aug 2001 15:10:40 -0500 (CDT) Date: Fri, 3 Aug 2001 15:10:40 -0500 From: John Stone To: chemistry@ccl.net Cc: John Stone Subject: Announce: VMD 1.7 Released Message-ID: <20010803151037.K21216@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i Dear CCL, VMD 1.7 is now available! Quick links: http://www.ks.uiuc.edu/Research/vmd/ (home page) http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ (VMD 1.7 page) Full announcement, followed by feature list: VMD "Visual Molecular Dynamics" 1.7 Announcement ------------------------------------------------ The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.7. VMD is a package for the visualization and analysis of biomolecular systems. VMD includes features for animation of molecular dynamics trajectories, interactive simulation, sequence browsing and structure highlighting, and powerful scripting capabilities. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for Compaq, IBM, HP, Linux, MacOS-X, Sun, and SGI Unix systems, as well as Microsoft Windows 95/98/ME/NT/2K. The VMD documentation includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. VMD development is supported by the NIH National Center for Research Resources. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ Links to magazine and journal articles about VMD are provided here: http://www.ks.uiuc.edu/Research/vmd/allversions/publications.html The authors request that any published work which utilizes VMD includes a reference to the VMD web page and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. The Theoretical Biophysics group encourages VMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. What's new in VMD 1.7? ---------------------- New Features o Integrated sequence browsing capabilities are now part of VMD, based on the previously available "ZoomSeq" Tcl script, with many improvements. The sequence browser is significantly faster than the older separately distributed ZoomSeq script, and will eventually provide several new interfaces not included in the production version. o Integrated Ramachandran plotting capabilities are now part of VMD. o Support for joysticks and other game controller input devices on the Windows platforms. o Windows versions of VMD now include support for VRPN, haptic feedback and interactive molecular dynamics. o Unix and Windows versions of VMD now include built-in support for Spaceball 6DOF 3-D controllers, which can be used for rotation, translation, and scaling. The Spaceball can be used simultaneously with the Mouse, so that one can use the mouse for picking, measuring, controlling of user interface menus, while using the Spaceball to orient the molecules in 3D. Future versions of VMD will make the Spaceball interface even more powerful. o New support for OpenGL ARB multisample antialiasing extension, provides multisample antialiasing on Linux/GeForce, Solaris/Expert3D and other platforms. o An easier-to-use -webhelper flag for use with Unix versions of VMD when setting up VMD as a web helper application for PDB files and VMD scripts. General Improvements and Bug Fixes o POV-Ray render export now provides basic support for orthographic views, with other renderers to follow. o Replaced O(N^2) hydrogen-bond finding code with a call to the bond search subroutine, resulting in a 2-4x speedup and better scaling. o Postscript scene exports now includes text labels o The axes are drawn using lines for Mesa builds of VMD. Mesa builds use software rasterization, so axis lines improve display redraws noticably. o Atom selection keywords lookups which operate on integer values now use a hash table to accelerate keyword list processing for a significant speed increase when working with large molecules. o Contains improvements donated by Sergei Izrailev, which make VMD more suitable for use as a library callable from within other applications. o Updated Tcl and Python callbacks to pass shift key state so that scripts like ZoomSeq can do more complex selection and highlighting. o The 'mol pdbload' and 'mol load webpdb' functions now download compressed PDB files from the RCSB, which is both faster and generally more reliable than downloading uncompressed files from the RCSB server. o New "phi" and "psi" angle atom selection keywords, which can be used to query and modify phi and psi angles. o Python commands can now be run with 'gopython -command "foo"' o Added "light pos" commands for setting the position of lights and restoring them to their default values o New "material delete" command o VMD is now built with Tcl 8.3.3 and Tk 8.3.3, which have improved support for secure http and many other omponents. o VMD is now built with Python 2.0.1 o VMD is now built with VRPN 6.0 o Rewritten MSMS interface, fixes PR 20 o Fixed PRs: 20, 157, 158, 159, 160, 161, 162, 163, 164, 165 User Interface Changes o All VMD file browsers are now implemented in Tk by default rather than FLTK, as Tk provides a much better match with the Win32 filesystem conventions. The FLTK file browser did not have a good Win32 interface (no drive letters) so it is now only used as a fall-back when Tk is not compiled into VMD. o The counters for selecting frames in the Edit form now range from 0 to the number of frames for the molecule, looping back to 0 or numframes-1 when the counters hit the end of the valid range. The "Skip" counter was renamed to "Step" and its range was limited to "1" or higher. o New sequence browsing window, and associated menus o Eliminated support for the old XForms GUI toolkit. o IRIX versions of VMD now use xterms instead of winterms, and they use the default font rather than Screen11 which used to cause some problems for people displaying remotely to non-SGI machines. User Documentation Updates o Added documentation for the "frame" atom selection keyword. o New molecular analysis section explaining how to use VMD for common analysis tasks, particularly those involving atom selections and molecule data. o Added documentation for new sequence browsing features o Added documentation for new Ramachandran plotting feature o Added documentation for new Spaceball and Joystick input devices on Windows and Unix. We are eager to hear from you, and thank you for using our software! John Stone vmd@ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078