From chemistry-request@server.ccl.net Fri Dec 22 15:31:08 2000 Received: from alien.biochem.wfubmc.edu (alien.biochem.wfubmc.edu [152.11.118.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA29184 for ; Fri, 22 Dec 2000 15:31:07 -0500 Received: from localhost (zhangxd@localhost) by alien.biochem.wfubmc.edu (SGI-8.9.3/8.9.3) with ESMTP id PAA24894; Fri, 22 Dec 2000 15:16:16 -0500 (EST) Date: Fri, 22 Dec 2000 15:16:15 -0500 From: Zhangxd To: xin_hu cc: Christian Pilger , amber@cgl.ucsf.edu, chemistry@ccl.net Subject: question on using amber In-Reply-To: <3A4397D5.6C43FA05@hotmail.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, when I use the amber6.0, the min.in is following, &cntrl the result is imin=1, maxcyc=20, ncyc=10, cut=10.0, ntpr=25, ntb=0, igb=1, &end and the result is wrong. NATOM = 4041 NRES = 243 MAXCYC= 20 NCYC = 10 NTMIN = 1 DX0 = 0.010000 DXM = 0.50000 DRMS = 0.00010 Water definition for fast triangulated model: Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2 Using modified Bondi radii and Tinker screening parameters Not enough memory: increase MATOM in nmr.h ~ please give me the reply. HAPPY CHRISTMAS! From chemistry-request@server.ccl.net Fri Dec 22 18:17:06 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA29802 for ; Fri, 22 Dec 2000 18:17:06 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id RAA15791; Fri, 22 Dec 2000 17:17:04 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id RAA14456; Fri, 22 Dec 2000 17:17:04 -0600 (CST) Date: Fri, 22 Dec 2000 17:17:04 -0600 From: John Stone To: vmd-l@ks.uiuc.edu, chemistry@ccl.net Subject: Announce: VMD 1.6 Released Message-ID: <20001222171658.A14408@geneseo.ks.uiuc.edu> Mail-Followup-To: vmd-l@ks.uiuc.edu, chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i VMD "Visual Molecular Dynamics" 1.6 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 1.6. VMD is a package for the visualization and analysis of biomolecular systems. This software is distributed free of charge and includes source code, documentation, and precompiled binaries for Compaq, IBM, HP, Linux, 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/ 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. We are eager to hear from you, and thank you for using our software! John Stone vmd at ks.uiuc.edu December 22, 2000 README file for VMD 1.6 --------------------------------------------------------------------------- What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/ --------------------------------------------------------------------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o No limit on the number of molecules, atoms, residues or number of animation frames, except available memory. o Many molecular rendering and coloring methods. o Stereoscopic display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Radiance, Raster3D, Rayshade, and Tachyon. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis. o Modular, extensible source code using an object-oriented design in C++, with a programmer's guide outlining the source code structure. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd VMD can be used to interactively display and control an MD simulation using NAMD. What's new in VMD 1.6? ---------------------- New Features o New "mol load webpdb XXXX" internet based PDB loading on both Windows and Unix platforms. o Python scripting interface available on Linux, Solaris, and IRIX versions o Wireframe rendering modes for MSMS and Surf (new control counter on the MSMS/Surf rep subforms) o Support for generation of RenderMan .RIB files from VMD scenes. o New platform support for Linux on Alpha processors o New platform support for Linux on PowerPC processors o Improvements supporting "VMD chat", a Tcl based collaborative VMD session feature to allow two or more people to connect their VMD sessions over a network. The "VMD chat" script is provided in the VMD script library. o Improvements supporting "ZoomSeq" sequence-based highlighting, selection, and coloring, as well as rudimentary internet based sequence search/query through new Tcl scripts, also to be found in the VMD script library soon after VMD 1.6 is released. General Improvements and Bug Fixes o Windows version of VMD now implements mouse capture so that you can drag the mouse outside of the graphics window while doing rotations, translations, scaling, and other mouse dragging operations. o Improved interactive rendering speed of molecular surfaces by a factor of two or more on most platforms. o Improved OpenGL materials rendering and gave VMD better looking default material properties. o Tachyon ray tracer binaries are now packaged along with VMD on all supported platforms. Now includes faster version of Tachyon. o Added the ability for Tcl code to capture VMD events as through the logfile mechanism, but through a Tcl variable, so that one VMD can easily remote control other VMD's through a bit of Tcl sockets code. o Significant speed increases for many common VMD commands, many commands are 5 to 200 times faster now, using new Tcl 8.x interpreter interface. o Made it easier to customize size/position of the VMD command window on Unix versions of VMD. o Improved VMD startup script, now works beter on HP-UX systems o No longer built with TclX/TkX, these are now removed from distribution. o Trimmed out excess baggage in VMD scripts directory o Built with FLTK 1.0.9 o Built with VRPN 5.01 o Fixed PRs: 60, 101, 106, 108, 109, 110, 111, 112, 113, 114, 124 User Interface Changes o New Tcl/Tk based RMSD fit GUI o Save state uses a GUI dialog now when possible. o The representation browser in the graphics form no longer lists the numbers associated with a draw style, to conserve space and improve readability. User Documentation Updates o Doucmentation for new Python scripting interfaces. o Updated various sections in User's guide, particularly relating to new rendering features, RMSD fit, etc. o Started lengthy update to Programmer's guide. o Added commit email capability to CVS, may make it an option for read-only CVS users as well. o significant improvements to Tcl scripting section Known bugs ---------- Please visit the VMD web site for information on known bugs, workarounds, and fixes: http://www.ks.uiuc.edu/Research/vmd/ Cost and Availability --------------------- VMD, NAMD, and BioCoRE represent the broad efforts of the Theoretical Biophysics group, an NIH Resource for Macromolecular Modeling and Bioinformatics, designed to develop and distribute free, effective tools (with source code) for molecular dynamics studies in structural biology. For more information, see: http://www.ks.uiuc.edu/Research/VMD/ http://www.ks.uiuc.edu/Research/NAMD/ http://www.ks.uiuc.edu/Research/biocore/ The VMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969). Disclaimer and Copyright ------------------------ VMD is Copyright (c) 1995-2000 the Board of Trustees of the University of Illinois and others. The terms for using, copying, modifying, and distributing VMD are specified in the file LICENSE. If you use VMD in a way you think is interesting or novel, we would like to know about it. The authors request that any published work which utilizes VMD includes a reference to the VMD web page: http://www.ks.uiuc.edu/Research/vmd/ 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. Documentation ------------- Three VMD manuals are available which describe how to install, use, and modify VMD. The VMD installation guide, is contained in the VMD distribution in the file "doc/ig.ps". The User's Guide and Programmer's Guide are available separately (due to size) from the VMD web site. Quick help may be accessed by pressing the "Help" button on the main VMD form, or by typing help in the VMD command window. This will bring up the VMD quick help page, and will lead you to several other VMD help files and manuals. Quick Installation Instructions ------------------------------- The Windows version of VMD is distributed as a self-extracting archive, and should be entirely self explanatory. Detailed instructions for compiling this version of VMD can be found in the installation guide. For quick installation of the binary distribution for Unix do the following: 1) uncompress and untar the distribution into a working directory. In this working directory, there are several subdirectories such as bin, src, doc, data, as well as this README and a configure script. Change to this working directory after the unpacking is complete. 2) Edit the file 'configure'; change the values for the $install_library_dir and $install_bin_dir to a directory in which vmd data files and executables should be installed: $install_bin_dir is the location of the startup script 'vmd'. It should be located in the path of users interested in running VMD. $install_library_dir is the location of all other VMD files. This included the binary and helper scripts. It should not be in the path. 3) A Makefile must be generated based on these configuration variables by running "./configure". 4) After configuration is complete, cd to the src directory, and type "make install". This will install VMD in the two directories listed above. Note that running "make install" twice will print error messages because you are attempting to overwrite some read-only files. This should be fine. 5) When installed, type 'vmd' to start (make sure the $install_bin_dir directory is in your path). Required Libraries ------------------ VMD requires several libraries and programs for various of its functions. In particular, it uses GL or OpenGL based 3-D rendering, and will require that you have the appropriate GL or OpenGL libraries on your system. Other programs are required by some of VMD's optional features. Please visit the VMD web site for more information: http://www.ks.uiuc.edu/Research/vmd/ VMD Development Team Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N. Matthews Urbana, IL 61801 TBG: http://www.ks.uiuc.edu/ VMD: http://www.ks.uiuc.edu/Research/vmd/ README for VMD; last modified December 22, 2000 by John Stone -- 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 at ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Fri Dec 22 18:23:33 2000 Received: from medicor.wustl.edu (medicor.wustl.edu [128.252.223.195]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA29822 for ; Fri, 22 Dec 2000 18:23:33 -0500 From: ReichertD@mir.wustl.edu Subject: AMBER6 and MPICH To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.1b September 30, 1999 Message-ID: Date: Fri, 22 Dec 2000 17:23:32 -0600 X-MIMETrack: Serialize by Router on Medicor/Washington University(Release 5.0.5 |September 22, 2000) at 12/22/2000 05:23:33 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi, I hope that someone out on the list can provide some help. I'm trying to compile AMBER 6 on a Linux cluster using MPICH, after a struggle I managed to get it to compile and the parallel version of sander runs fine, gibbs is another story. Every time gibbs is executed I get the following message: Fatal error; unknown error handler May be MPI call before MPI_INIT Error message is MPI_ABORT and code is 197 I have to admit to being stumped as to what to try next. In case it helps the kernel is 2.2.12 SMP, compiler is egcs-2.91.66, and I'm using MPICH 1.2.0. As I mentioned sander works, only gibbs is failing. Hope someone can provide some guidance. Happy Holidays, -david David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd@mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 From chemistry-request@server.ccl.net Fri Dec 22 21:34:22 2000 Received: from swan.prod.itd.earthlink.net (swan.prod.itd.earthlink.net [207.217.120.123]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA30464 for ; Fri, 22 Dec 2000 21:34:22 -0500 Received: from piglet (dialup-63.215.113.66.Chicago1.Level3.net [63.215.113.66]) by swan.prod.itd.earthlink.net (EL-8_9_3_3/8.9.3) with SMTP id SAA02993 for ; Fri, 22 Dec 2000 18:34:11 -0800 (PST) From: "Slawomir Z. Janicki" To: "CCL" Subject: RE: gamess people play on the pc Date: Fri, 22 Dec 2000 20:30:47 -0600 Message-ID: <000101c06c88$5b6a0240$4271d73f@piglet> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAAB7D@lvlxch01.unitedcatalysts.com> X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 I have been using PC-GAMESS for over two years now. It really enabled me to run MCSCF calculations that were impossible to setup under the Unix version of GAMESS due to disk space constrains. An AOINTS file that would not fit on a 2GB partition under Unix was compressed to little over 200 MB on a PC. I don't know of any program to transfer the guess orbitals (I think this is what you are asking about) from Gaussian to GAMESS, but I am sure something like this exists in this universe. Transferring the Cartesian coordinates is a snap, but the z-matrices work somewhat differently in these programs. You can't use the redundant coordinates in GAMESS like in Gaussian, I have not investigated further. You have access to the same basis sets in Gaussian and GAMESS, if something you need is not coded in, you can download your preferred basis set off the Web and copy it to the input file. In terms of resources I think that PC-GAMESS makes a better use of a PC than Gaussian. I have used PC-GAMESS efficiently on PCs with four CPUs and I know of installations that run distributed version of PC-GAMESS on as many as 512 CPUs. I don't know how the scaling compares to G98/Linda/Linux or GAMESS/Beowulf/Linux, but on a single machine PC-GAMESS beats WinG98 any time. I have mentioned the compression of the scratch files which really reduces disk I/O for the price of minor increase of CPU usage. Overall, the wall clock time is substantially reduced. For operating system you really want WinNT4.0 or Win2000. Win98 or WinME will give you a lot of grief :(. Depending on your finances/particular calculations you may want to invest in a two-CPU machine (a PC with two Celeron CPUs can be built for little money even though Intel maintains it can't be done), EIDE-RAID controller (a $75 ATA/100 RAID controller + two $100 7200 rpm 20GB ATA/100 disks make a very efficient subsystem) or DDR memory. Slawomir Janicki janicki1@earthlink.net -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Shobe, Dave Sent: Friday, December 22, 2000 10:20 AM To: 'CCL' Subject: CCL:gamess people play on the pc I'm considering downloading Gamess-US for Windows (even though it will probably take an entire day with my modem), because it has more multireference options that Gaussian. 1. Have any of you done this, and would you recommend it? 2. Are there utilities that can transfer information (basis sets, wavefunctions, etc.) between Gamess and Gaussian? 3. How do Gamess and Gaussian compare as regards time and resource use on a PC? --David -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net