From chemistry-request@server.ccl.net Sat Nov 20 09:54:38 1999 Received: from ecstasy.ksu.ru (ecstasy.ksu.ru [193.232.252.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03393 for ; Sat, 20 Nov 1999 09:54:36 -0500 X-Pass-Through: Kazan State University network Received: from chem-54.ksu.ru (localhost [127.0.0.1]) by ecstasy.ksu.ru (8.9.3/8.9.3) with ESMTP id NAA23503 for ; Sat, 20 Nov 1999 13:26:34 +0300 (MSK) Date: Sat, 20 Nov 1999 13:26:32 +0300 From: gshamov X-Mailer: The Bat! (v1.34a) UNREG / CD5BF9353B3B7091 Reply-To: gshamov Organization: ksu X-Priority: 3 (Normal) Message-ID: <1560.991120@ksu.ru> To: chemistry Subject: what is Titan ? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCLers, Does anyone have experience using "Titan" program? I'm cosidering to buy it, and i'm very interesting in the following topics: 1. Have Titan full functionality of Jaguar ( GVB, etc. ) or only limited subset of it? 2. The Titan's precursor, Spartan, is copy-protected with HASP. Is Titan copy-protected with HASP too? Any answersn will be gratefully pleased. Best regards, G.A.Schamov postgraduate student of Dept.Org.Chem. Kazan State Univ. mailto:gshamov@ksu.ru From chemistry-request@server.ccl.net Sat Nov 20 11:18:09 1999 Received: from panix3.panix.com (k2fmzgChVuljh0vRRxC09fUA/1dciDR2@panix3.panix.com [166.84.0.228]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03863 for ; Sat, 20 Nov 1999 11:18:09 -0500 From: kynn@panix.com Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id KAA28004; Sat, 20 Nov 1999 10:14:07 -0500 (EST) Date: Sat, 20 Nov 1999 10:14:07 -0500 (EST) Message-Id: <199911201514.KAA28004@panix3.panix.com> To: CHEMISTRY@ccl.net Subject: Restraining potentials for umbrella sampling In all accounts of umbrella sampling I've seen, the restraining potentials, when given, are invariably harmonic in the reaction coordinate. However, it would be computationally cheaper (specially when the simulation method requires computing forces) to make this potential flat in the region of interest. I.e., (x - x0)^2, if |x - x0| > h V(x) = h^2, if |x - x0| <= h ; This potential V is flat if the reaction coordinate x lies in the interval [x0 - h, x0 + h], and grows quadratically otherwise. (Linear "walls" instead of quadratic ones lead to other problems, because they don't penalize far-out conformations sufficiently unless one makes the walls practically vertical; this would preclude even minor excursions out of the window, which would be undesirable, since such excursions may sometimes be necessary to adequately sample the desired window.) Does anybody know of any serious drawback with the "flat-bottom" scheme described above? Thanks KJ From chemistry-request@server.ccl.net Sat Nov 20 15:36:13 1999 Received: from hal.icqem.pi.cnr.it (hal.icqem.pi.cnr.it [131.114.203.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04874 for ; Sat, 20 Nov 1999 15:36:12 -0500 Received: (from guido@localhost) by hal.icqem.pi.cnr.it (8.9.1/8.9.1) id UAA30070; Sat, 20 Nov 1999 20:30:49 +0100 Date: Sat, 20 Nov 1999 20:30:49 +0100 From: Guido Germano Message-Id: <199911201930.UAA30070@hal.icqem.pi.cnr.it> To: chemistry@ccl.net, help@gaussian.com Subject: MP2+freq and pop=nbo problems with g98 on SGI Cc: guido@hal.icqem.pi.cnr.it Hello! Recently I recompiled g98 Rev. A6 on a SGI Origin 2000 (IRIX 6.5.5f and 7.3 compilers). After this, pop=nbo doesn't work any more. The same jobs that took less than 1 minute with the binaries generated by the 7.2.1.2m compilers now stay in for 30 hours in l607 without exiting. The same happens with Rev. A7, that however I didn't try with the old compilers. Another problem common to both revisions and to both compilers is that jobs requiring MP2 frequencies crash. Sometimes there is a request for an unreasonable amount of memory, sometimes just a sentence mentioning an error, sometimes nothing more than a core dump. The same jobs run fine on a DEC with the same 1 GB of RAM and less disk space. The only MP2 frequencies I was able to get on the Origin were from diatomics. Thank you and regards Guido Germano http://hal.icqem.pi.cnr.it/germano From chemistry-request@server.ccl.net Sat Nov 20 15:56:55 1999 Received: from mail4.nycap.rr.com (mail4-0.nyroc.rr.com [24.92.32.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04984 for ; Sat, 20 Nov 1999 15:56:55 -0500 Received: from claessen.nycap.rr.com ([24.29.72.27]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com; Sat, 20 Nov 1999 14:54:37 -0500 Reply-To: From: "Rolf Claessen" To: "gshamov" , "chemistry" Subject: RE: what is Titan ? Date: Sat, 20 Nov 1999 14:49:30 -0500 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: <1560.991120@ksu.ru> X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Dear Dr. Schamov, our researchgroup just purchased Titan recently. As far as I know, Titan has the full functionality of Jaguar and it is also hardware protected. Rolf Claessen http://www.claessen.net > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of gshamov > Sent: Saturday, November 20, 1999 5:27 AM > To: chemistry > Subject: CCL:what is Titan ? > > > Hello CCLers, > Does anyone have experience using "Titan" program? > I'm cosidering to buy it, and i'm very interesting in the > following topics: > > 1. Have Titan full functionality of Jaguar ( GVB, etc. ) or only > limited subset of it? > 2. The Titan's precursor, Spartan, is copy-protected with HASP. Is > Titan copy-protected with HASP too? > > Any answersn will be gratefully pleased. > > Best regards, > G.A.Schamov > postgraduate student of > Dept.Org.Chem. > Kazan State Univ. mailto:gshamov@ksu.ru > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Sat Nov 20 17:07:00 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05304 for ; Sat, 20 Nov 1999 17:06:59 -0500 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id NAA17642 for ; Sat, 20 Nov 1999 13:00:49 -0800 (PST) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0) with SMTP id NAA294255 for ; Sat, 20 Nov 1999 13:00:49 -0800 (PST) Date: Sat, 20 Nov 1999 13:00:48 -0800 (PST) From: Maneesh Yadav To: chemistry@ccl.net Subject: Re: Linux Autodock 3.01, My bad Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Sorry about the post, all I did was delete the object files that came with the distribution (which I assume were SGI object files, but funny thing is that the library is still malformed, but the dist_3.0 one is fine, not that it matters) and the makefile works fine. Thanks for the help, Maneesh From chemistry-request@server.ccl.net Sat Nov 20 21:27:08 1999 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA06273 for ; Sat, 20 Nov 1999 21:27:02 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Sun, 21 Nov 1999 09:25:35 +0800 Sender: user@ccl.net Message-ID: <380D0BA3.4F26C57E@iris.sipp.ac.cn> Date: Wed, 20 Oct 1999 09:24:03 +0900 From: mao xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary: compilation problem of NBO Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi: I have sent an email about compilation problem of NBO, I got the great help from Dr. Eric Glendening and Dr. Fred P. Arnold. Here is the solution for my problem. >From Fred: -------------------- There should be a file with it called 'activate.f', or some such, which is used to cut out the specific version of NBO you need (standalone, Gaussian Modules, Mopac Modules, etc). It should be in the same directory you got the program from. Most commercial packages, (Gaussian, Jaguar, Spartan) have NBO built it, but they cost real money. -fred ------------------------------------------------------------- >From Dr. Eric: ------------------------ Don't copy nbo.src to nbo.f and compile. nbo.src contains source code for the standalone version of NBO and for interfaces to programs like GAMESS and Gaussian. These lines of nbo.src have been commented out. The preprocessor program (Enable.f) that should have come with the NBO source code must be used to activate a version of NBO before compilation. Compile Enable.f. Run Enable to activate one of the NBO versions, presumably the standalone, GENNBO. Compile the resulting gennbo.f file. ---------------------------------------------- The following is another question about NBO, and the answer from Eric is: > I got the error: > ----------------------------------------------- > ld: WARNING 85: definition of shmdt_ in GENNBO.o preempts that > definition in /usr/lib/libftn.so. > ld: WARNING 47: This module contains branch instruction(s) that might > degrade performance on an older version (rev. 2.2) R4000 processor. > ---------------------------------------------------------- I suspect that this is only a warning that one of the NBO routines (SHMDT) has the name as that in the fortran library. Do you get an executable? If so, it's probably fine. If not, you might go through nbo.src and rename all occurences of SHMDT to, say, SHMIDT, then recompile. > And when I generate the AMPNBO.FOR, I compiled it with f77 -o ampnbo > ampnbo.for, I got the error of "Cannot open file SIZES". So would you > please give me more suggestion about my problem. Thank you. AMPNBO is not a standalone code. It must be interfaced to the AMPAC program. SIZES is the AMPAC file that defines version program parameters. ------------------------------ Thank Dr. Eric and Dr. Fred again. Regards, Mao Xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~