From UDIM018%FRORS31.BITNET@phem3.acs.ohio-state.edu Fri Jul 9 10:37:51 1993 Date: Fri, 09 Jul 1993 14:37:51 -0400 (EDT) From: UDIM018%FRORS31.BITNET@phem3.acs.ohio-state.edu Subject: AMSOL Solvation Free energies on ions. To: chemistry@ccl.net Message-Id: <01H0BZBZV2C29H0M5R@phem3.acs.ohio-state.edu> E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-44-27-41-17 (lab);44-27-38-66(University) e-mail UDIM018 at FRORS31.BITNET I have some odd observations on AMSOL. In checking a SM1 calculation on AMPAC 4. on the molecule OH(-), starting geometry of 1.00 and the control card AM1 SM1 DERINU PRECISE CHARGE=-1 TRUES HGAS=-14.115617 I found a RS/6000/320h computation time of 42 seconds and a final free energy of solvation of -109.1 kcal if the oxygen atom is read in first, the hydrogen second. The computation time goes to 391 seconds and an energy of -109.5 is obtained if H is read in first, oxygen second! The literature value is -109.2. Normally one would read in the heavy atoms first in a calculation. The energy difference is no big deal, the computational time is! Is it possible that some of the very long computational times in AMSOL are due to atom sequencing? Per another curiosity, most of the monocation and monoanions experimental solvation free energies are in the 50-100 kcal/mol region, a few edge just above like OH(-), F(-), etc. However, one structure we are looking at is PO3(-) which is isoelectonic with NO3(-) but has much difference charge characteristics. (the oxygens are more negative and the phosphorous more positive than the corres atomns in NO3(-)). One would expect a solvation free energy larger than NO3(-) (exptl around -65 and approximated in SM1, SM2 and SM3 at -65, -59 and -48 respe However, SM1, SM2, and SM3 give values of -178, -144, and -99 respectively. One ab initio model gives -78 which is about where I might have guessed. The -178 and -144 values look "odd". So far from what we have done on other phosphorous containing system modeling ATP or something like that using SM1 and SM2 questionable (see also Cramer and Truhlar's paper in J. Comp-Aided Molecular Design, 6, 629 (1992), Table 7, p649.) Any comments? From zrfl0128@awshp.rus.uni-stuttgart.de Fri Jul 9 09:55:04 1993 From: zrfl0128@awshp.rus.uni-stuttgart.de (Dr. Heinz Poehlmann) Message-Id: <9307091307.AA26364@awshp.rus.uni-stuttgart.de> Subject: DENSITY Program requested To: CHEMISTRY@ccl.net Date: Fri, 9 Jul 93 15:07:31 DST Dear Netters, I am looking for a "standard" Fortran version of the DENSITY program package. It's an add on of the famous MOPAC to display electron density contours, orbitals etc.... out of MOPAC results. I have an old DEC VAX-specific Fortran version, which looks to be horrible to transfer to any other (UNIX) platform. There seems to exist more than one version of the program, with different graphics libraries used. Any help would be appreciated. Thanks in advance, Heinz Poehlmann .-------------------------------------------------------------------------. | Dr. Heinz W. Poehlmann Regionales Rechenzentrum | | Computational Chemistry & Visualization der Universitaet Stuttgart | | e-mail: poehlmann@rus.uni-stuttgart.de Abt. Anwendungssysteme | | phone: (49)-711-685-5992 Allmandring 30 | | fax: (49)-711-6787626 D-70550 Stuttgart , Germany | '-------------------------------------------------------------------------' From mizan%beaker.engin.umich.edu@srvr2.engin.umich.edu Fri Jul 9 06:48:36 1993 From: Date: Fri, 9 Jul 93 10:48:36 EDT Message-Id: <9307091448.AA17529@beaker.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: BAC-MP4 Hi Netters, Does anybody know what "quantum chemical BAC-MP4 calculations" are ? Who wrote the program ? Any references ? Thanks in advance. Tahmid From J_BROWN@uvmvax.uvm.edu Thu Jul 8 07:30:00 1993 Date: Thu, 8 Jul 1993 12:30 EST From: J_BROWN@uvmvax.uvm.edu Subject: Requesting help with MM3(93) nitrogen inversion drivers To: chemistry@ccl.net Message-Id: <01H0AT0DEKCW000QMH@uvmvax.uvm.edu> Could someone please tell me how to do nitrogen inversion drivers with MM3(92) in standalone mode (eg., without the Sybyl interface). I need to known what lines of the input file are to be altered and/or added to the MM3(92) input file. Could you include input file column and line numbers in the explanation. Thank you very much, Jay Brown From braendle@iacrs1.unibe.ch Fri Jul 9 21:06:35 1993 From: braendle@iacrs1.unibe.ch (Martin Braendle) Message-Id: <9307091706.AA20916@iacrs1.unibe.ch> Subject: Email address of A.C. Hess, Richland To: chemistry@ccl.net Date: Fri, 9 Jul 1993 19:06:35 +0200 (NFT) Sorry for wasting the bandwidth, but netfind did not give an answer. Does anybody know the E-mail adress of Anthony C. Hess, Pacific Northwest Laboratory, Richland, Washington (Periodic Hartree-Fock studies on alumninosilicates and on metal oxide surfaces)? Thank you. Martin Braendle -------------------------------------------------------------------------------- Martin Braendle, Institute for Inorganic and Physical Chemistry, University of Berne, Freiestr. 3, CH-3012 Berne, Tel. xx41 31 65 42 25, Fax xx41 65 39 94, Email braendle@iacrs1.unibe.ch (or braendle@iac.unibe.ch) -------------------------------------------------------------------------------- From DSMITH@uoft02.utoledo.edu Fri Jul 9 08:01:10 1993 Date: Fri, 09 Jul 1993 13:01:10 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: which brand of workstation? To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu Message-Id: <01H0C85K6KQG0004M5@UOFT02.UTOLEDO.EDU> As the hardware and software for molecular modeling continue to evolve, choices seem to get harder when deciding which platform to buy. That is, until recently.... When MacroModel 4.0 was announced, apparently all platforms except SGI were dropped (there had been versions for HP and DEC in the works, supposedly). Certainly SGI is not the fastest hardware available, even with the new 4400-based cpu and parallel architectures (and what software is really taking advantage of that yet?). Why does SGI dominate still? Why is commercial software only written for SGI - or if I am wrong, as I hope I am, what other workstations are commercial vendors writing for? There are two types of software and two types of hardware, to make things simple. First is number crunching -- typically we are talking about non- graphical programs or portions thereof, on IBM R6000 or DEC Alpha boxes, I assume. The second are for graphics, and SGI seems to be the only player left. What about HP, SUN, DEC with Kubota graphics, IBM, or any others? What is it that users (and commercial vendors/developers) want that only SGI seems to supply? Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From shenkin@still3.chem.columbia.edu Fri Jul 9 10:59:40 1993 Date: Fri, 9 Jul 93 14:59:40 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9307091859.AA05707@still3.chem.columbia.edu> To: "DR. DOUGLAS A. SMITH, Subject: Re: which brand of workstation? Doug Smith wrote: > When MacroModel 4.0 was announced, apparently all platforms except SGI were > dropped .... This is completely false. We continue to support IBM RS-6000, and have never said or implied otherwise. We have no plans or even thoughts of plans to discontinue support for IBM RISC. You may take this as an offical statement by the MacroModel developers. The opinions expressed below this line, however, are personal. > ...Why does SGI dominate still? In the chemical/graphics world the answer is simple: GL. IBM RISC is also a contender for the same reason: GL. If they have been less of a contender than SGI, it's because their GL implementation is (naturally) not as good as SGI's; on the whole, it's been slower, and DGL is not (to my knowledge) available. In my humble opinion, IBM's market penetration has also been impeded by the fact that their UNIX is more different from everyone else's than everyone else's is from each other's. (I didn't say worse and I don't mean worse -- I just said different. No flames, please.) OpenGL might change all this, and make existing applications easily portable to other platforms -- provided the OpenGL implementations are good. In my opinion (again), the market penetration of new platforms will depend strongly on users' ability to obtain existing common software package on them; by this I mean the packages that already run on SGI and IBM RISC. OpenGL would also allow the many skilled graphics programmers out there who have come to know and love GL to apply their skills in a manner that will make newly written programs run well across a wide variety of architectures. But OpenGL is in its infancy, and "time will tell" whether it will pan out. > There are two types of software and two types of hardware, to make things > simple. First is number crunching -- typically we are talking about non- > graphical programs or portions thereof, on IBM R6000 or DEC Alpha boxes, > I assume. Such software is typically available on many platforms; for example, Gaussian-92 is available on Suns, HP, DEC, as well as Cray and the aforementioned machines; also on others I've not mentioned. It's simply easier to support software that does not do graphics (or audio) across many platforms, though there may be non-trivial numerical and OS-interaction issues to contend with. Pure X graphics lies, in ease of portability, between numerical code and code that tries to make use of hardware-accelerated 3D graphics. Back to MacroModel/BatchMin for the moment. We have not precluded supporting BatchMin on other platforms in the future; a lot depends on what our customers request. My guess is that the reason our customers have not been pounding the doors down with requests for BatchMin support on other machines is that people typically want to use it with MacroModel, and MacroModel performs best on a GL machine. Once you've got the first SGI or RS-6000, it's easier to buy a second than to go to a whole new architecture; for one thing, whoever has to manage the machines will have an easier time. For another, it's helpful to use the same machine that your friends use -- then you always have people to go to to help you out. After a few years one gets a bit jaundiced by the revelation that machine X has the fastest CPU this year. The differences in speed are not that great, and speed-per-dollar is also a consideration. Maintainability and support and availability of software tools also counts for a lot. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ************** The cost of flexibility is incomprehensibility. ************** From pbays@saintmarys.edu Fri Jul 9 21:18:59 1993 Date: Fri, 9 Jul 1993 16:18:59 +0500 () From: Phil Bays Subject: Workstations To: chemistry@ccl.net Message-Id: I am interested in Doug's questions about hardware platforms. I am negotiating with HP for hardware; in fact they are putting a test machine in my office next week. But I am concerned about what software I will be able to use next year and the year after. Tripos seems to not want to touch HP; MacroModel has apparently dropped it (see Doug's note). MSI has software on HP but very expensive, even with academic discounts, and WaveFunction seems committed to HP. But my problem is that once I get hardware, even if given to me, I will have a hard time convincing someone (granting agency or my Dean) that I need more "because no software runs on it!" Phil Bays Chemistry Saint Mary's College Notre Dame IN 46556 From shawn@wucmd.wustl.edu Fri Jul 9 13:43:37 1993 Date: Fri, 9 Jul 93 18:43:37 -0500 From: shawn@wucmd.wustl.edu (Shawn Huston) Message-Id: <9307092343.AA22097@wucmd> To: chemistry@ccl.net Subject: CCP5 Quarterly I am looking for a number of articles that appear in the journal CCP5 Quarterly. Can somebody give me the name of a library that gets this journal? Does anyone know what CCP stands for? Any help would be greatly appreciated. shawn@wucmd.wustl.edu