From jkl@ccl.net Sun Apr 20 00:32:29 2003 -0400 From: "Vivek Raut" To: jkl@ccl.net Subject: Tinker in parallel processing? Date: Sun, 20 Apr 2003 10:02:28 +0530 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: Hello, I have been recently introduced to Tinker which I intend to use for protein -material interaction simulation. I would like to know if I can use Tinker on a parallel processing network (Beowulf clusters, so that I can use the umbrella sampling technique to carry out the simulations. We have the infrastrcture for it. If yes, then how should I configure the system? Kindly pass this mail to the CCL. Thank you, Vivek. ********************************************************************** Vivek Raut Graduate Research Assistant Bioengineering Dept. Clemson University, Clemson, SC-29631 Email:vraut@clemson.edu Phone:864-650-1431. ********************************************************************* "The future belongs to those who believe in the beauty of their dreams."- Eleanor Roosevelt _________________________________________________________________ Windows Server 2003. Do more with less. http://www.msn.co.in/computing/winsvr2003/ Upgrade now! From chemistry-request@server.ccl.net Sun Apr 20 05:14:09 2003 Received: from yangtze.hku.hk ([147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3K9E8a17649 for ; Sun, 20 Apr 2003 05:14:09 -0400 Received: from localhost (xzheng@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h3K9RfN24183 for ; Sun, 20 Apr 2003 17:27:41 +0800 Date: Sun, 20 Apr 2003 17:27:41 +0800 (HKT) From: Zheng Xiao To: CCL Subject: Electric field in MOPAC97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am feeling puzzled with the electric field treatments in MOPAC97. For a system containing several carbon atoms, I sent a job with keywords like : { ... ... XYZ FIELD(-0.0020,0.0,0.0) DEBUG HCORE ... ... C 10088.48320578 0 -2.40518899 0 -1.81922895 0 ( this is the first line specifying the coordinates in Cartesian format) ... ... } By checking the output file, the first element of single-electron integral is -1.520379*1.d3 eV. And deleting the FIELD keyword results in the corresponding value as -1.517857*1.d3 eV. The difference is -2.522 eV which certainly comes from 10088.48320578*(-0.0020)/8.d0. But I think it is clear that in semiempirical methods the integral should amounts <2S(C)|Ex*x|2S(C)> = Ex*x(C) = 10088.48320578*(-0.0020). So I'm wondering why the factor 1/8.d0 exists here, and by looking into the source code, it seems that this factor relates somehow to the internal unit transformation process. But I don't think it is reasonable to appear in the subsequent calculation. Is it a bug? or simply a problem with my copy? or anything to do with the theory? I would like to have your advice. All comments are welcome. Thanks in advance. Best wishes, Zheng Xiao -- C---------------------------------------C C Zheng Xiao C C Ph.D. Candidate C C Department of Chemistry C C University of Hong Kong C C---------------------------------------C