From bakasov@ictp.trieste.it Tue Oct 29 04:32:46 1996 Received: from ictpsp6.ictp.trieste.it for bakasov@ictp.trieste.it by www.ccl.net (8.8.0/950822.1) id DAA26749; Tue, 29 Oct 1996 03:48:12 -0500 (EST) Received: (from bakasov@localhost) by ictpsp6.ictp.trieste.it (8.6.9/8.6.9) id JAA27116; Tue, 29 Oct 1996 09:45:21 +0100 Date: Tue, 29 Oct 1996 09:45:19 +0100 (MET) From: Bakasov Ayaz To: CHEMISTRY@www.ccl.net Subject: Se and Te: all-electron basis sets wanted Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, we hope that some of you know the answer to our question. We would greately appreciate help. There is a great need for all-electron basis set(s) for Se and Te (ideal is further continuation to Po). While 6-311G** for Se is found in Gaussian94, does someone know anything about all-electron (non-CEP) basis sets for Te ? More generally, are there around all-electron basis sets (may be even unpublished - we would gratefully cite any source which provides us with them) for the 3rd and 4th rows, good quality ones?! The nature of the problem we are dealing with allows us not care (for the moment) about relativistic effects. Answers will, naturally, be summarized and posted. Sincerely, Ayaz Bakasov. From chem8@york.ac.uk Tue Oct 29 07:32:47 1996 Received: from lendal.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.0/950822.1) id HAA27621; Tue, 29 Oct 1996 07:07:36 -0500 (EST) Received: from ebor.york.ac.uk by lendal.york.ac.uk with SMTP (PP); Tue, 29 Oct 1996 11:59:09 +0000 Received: from localhost by ebor.york.ac.uk via SMTP (950511.SGI.8.6.12.PATCH526/940406.SGI) id MAA27930; Tue, 29 Oct 1996 12:04:22 GMT Date: Tue, 29 Oct 1996 12:04:22 +0000 (GMT) From: John Waite Reply-To: John Waite To: Bakasov Ayaz cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:Se and Te: all-electron basis sets wanted In-Reply-To: Message-ID: MIME-Version: 1.0 Content-type: text/PLAIN; charset="US-ASCII" Hi Ayaz, I am currently optimising triple zeta + bases for the main group elements of row 4 of the Periodic Table, together with all of row 5 to be published when completed. So below are my Se and Te, all-electron bases. You could also look in Huzinaga's 'Green book' and the bases of Harry Partridge. Trusting these help and good luck, John Se (18S13P7D) SCF OPT 0,3 Se 0.0 0.0 0.0 Se 0 S 1 1.0 5.967005500219366D+05 1.0 S 1 1.0 8.941849869576445D+04 1.0 S 1 1.0 2.034605218420411D+04 1.0 S 1 1.0 5.761621923999998D+03 1.0 S 1 1.0 1.880030507510481D+03 1.0 S 1 1.0 6.789139209999996D+02 1.0 S 1 1.0 2.648532010000001D+02 1.0 S 1 1.0 1.085390973376053D+02 1.0 S 1 1.0 3.385267425452839D+01 1.0 S 1 1.0 1.451335493389040D+01 1.0 S 1 1.0 4.407956588545337D+00 1.0 S 1 1.0 1.921579066534049D+00 1.0 S 1 1.0 4.723963358826513D-01 1.0 S 1 1.0 1.714541000000000D-01 1.0 P 1 1.0 4.534604708969906D+03 1.0 P 1 1.0 1.075013510509206D+03 1.0 P 1 1.0 3.470411079801183D+02 1.0 P 1 1.0 1.309713099908095D+02 1.0 P 1 1.0 5.403844308692906D+01 1.0 P 1 1.0 2.349734849613973D+01 1.0 P 1 1.0 1.028897474262754D+01 1.0 P 1 1.0 4.346917917456898D+00 1.0 P 1 1.0 1.798287898022591D+00 1.0 P 1 1.0 6.334269468082617D-01 1.0 P 1 1.0 1.677728814830268D-01 1.0 D 1 1.0 1.547901434229183D+02 1.0 D 1 1.0 4.568957701866580D+01 1.0 D 1 1.0 1.667547118736933D+01 1.0 D 1 1.0 6.572134829845468D+00 1.0 D 1 1.0 2.579553965204672D+00 1.0 D 1 1.0 9.309232744872770D-01 1.0 GTO BASIS FOR Te STATE: 3P J.WAITE, THE NATIONAL HELLENIC RESEARCH FOUNDATION, ORGANIC CHEMISTRY INSTITUTE, VAS. KONSTANTINOU 48, ATHENS 116-35, GREECE L EIGENVALUES EXPONENTS COEFFICIENTS S -1131.6248 -173.4570 -36.4520 -7.3417 -1.2970 4.686262020789758D+06 0.000045 -0.000014 -0.000006 0.000003 0.000001 7.016868814397455D+05 0.000347 -0.000112 -0.000050 0.000022 0.000008 1.594284344585404D+05 0.001825 -0.000594 -0.000263 0.000117 0.000041 4.505156433444189D+04 0.007662 -0.002498 -0.001112 0.000495 0.000174 1.466546710745936D+04 0.027159 -0.009019 -0.004003 0.001788 0.000630 5.293449069889583D+03 0.081764 -0.028046 -0.012590 0.005611 0.001974 2.071488892490748D+03 0.199740 -0.075403 -0.034017 0.015266 0.005391 8.648225051737021D+02 0.353503 -0.160585 -0.075442 0.033859 0.011918 3.798494284487395D+02 0.350329 -0.233983 -0.114426 0.052551 0.018684 1.723591002192273D+02 0.120730 -0.042372 -0.027051 0.011781 0.003954 7.615257907707930D+01 0.004167 0.530471 0.410996 -0.202544 -0.072303 3.528391300947559D+01 0.000799 0.560733 0.592490 -0.331557 -0.123287 1.358378488881609D+01 -0.000533 0.086628 -0.484531 0.386804 0.156683 6.892535550852062D+00 0.000282 -0.015477 -0.801251 0.897493 0.374551 2.487688144258547D+00 -0.000121 0.004818 -0.094142 -0.623719 -0.349451 1.176908378195005D+00 0.000061 -0.002284 0.013959 -0.796003 -0.673224 2.822602850556357D-01 -0.000018 0.000671 -0.003663 -0.041117 0.761473 1.345070084820375D-01 0.000009 -0.000304 0.001642 0.011029 0.533963 P -162.4357 -31.7799 -5.6449 -0.9907 1.445156080906941D+04 0.000760 -0.000351 0.000152 -0.000049 3.426062274582398D+03 0.006531 -0.003057 0.001310 -0.000419 1.109981592292776D+03 0.034647 -0.016375 0.007107 -0.002283 4.218838717388739D+02 0.127100 -0.062993 0.027279 -0.008742 1.768991500527563D+02 0.310446 -0.162688 0.072339 -0.023346 7.901069394640879D+01 0.427742 -0.243802 0.107583 -0.034513 3.663610677412699D+01 0.241058 -0.002930 -0.010630 0.003823 1.641185293694340D+01 0.032153 0.533798 -0.355065 0.123127 7.675309179937873D+00 -0.000535 0.498025 -0.295985 0.096827 3.057236183539741D+00 0.000156 0.070629 0.559793 -0.251349 1.295612122303268D+00 -0.000143 -0.005278 0.609921 -0.300884 3.827472687519649D-01 0.000029 0.001922 0.061103 0.484671 1.535170981012005D-01 -0.000011 -0.000738 -0.009601 0.668716 D -23.2040 -2.7270 3.615666534951539D+02 0.015318 -0.006135 1.074509086450790D+02 0.104706 -0.043563 3.973675071733074D+01 0.333309 -0.137294 1.589843016194811D+01 0.500075 -0.201128 6.578891273209935D+00 0.257789 0.098339 2.463299308457708D+00 0.020053 0.607027 8.532188781822235D-01 -0.000160 0.445375 ENERG= -0.6610704809530200D+04, VIR= -0.19999987D+01, P.E.=-.1322141830D+05, K.E.=0.6610713487D+04, Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* rosen@cyclades.nrcps.ariadne-t.gr Organic and Pharaceutical Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece From Leon.Dupont@ulg.ac.be Tue Oct 29 08:32:59 1996 Received: from aix4.segi.ulg.ac.be for Leon.Dupont@ulg.ac.be by www.ccl.net (8.8.0/950822.1) id IAA28067; Tue, 29 Oct 1996 08:29:05 -0500 (EST) Received: from dupont (dupont.cris.ulg.ac.be [139.165.104.21]) by aix4.segi.ulg.ac.be (8.7.6/8.6.10) with SMTP id OAA22570 for ; Tue, 29 Oct 1996 14:28:09 +0100 Message-Id: <1.5.4.16.19961029142819.1e372cfc@pop3.mailst.ulg.ac.be> X-Sender: u003290@pop3.mailst.ulg.ac.be X-Mailer: Windows Eudora Light Version 1.5.4 (16) Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Tue, 29 Oct 1996 15:28:19 +0100 To: chemistry@www.ccl.net From: Leon Dupont Subject: copy of screen view with SYBYL software Dear netters, I am using the SYBYL software on a Silicon Graphics Indigo. How could I get an exact printed copy of the screen view? Postscript output included in Sybyl transforms the original view which is seen on the screen. Thank you. L. Dupont ____________________________________________________________________ Dupont L=E9on | e-mail: Leon.Dupont@ulg.ac.be Unit=E9 de Cristallographie | tel.: +32-4-366.37.62 Institut de Physique Bat. B5 | fax: +32-4-366.23.55 Universit=E9 de Li=E8ge au Sart-Tilman | B 4000 LIEGE (Belgium) | http://www.ulg.ac.be/physexpe/crist/ ____________________________________________________________________ From dlarson@elara.tripos.com Tue Oct 29 11:32:50 1996 Received: from gatekeeper.tripos.com for dlarson@elara.tripos.com by www.ccl.net (8.8.0/950822.1) id LAA29406; Tue, 29 Oct 1996 11:16:24 -0500 (EST) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id KAA17187; Tue, 29 Oct 1996 10:13:40 -0600 Received: from elara.tripos.com(192.160.145.60) by gatekeeper.tripos.com via smap (V1.3) id sma017182; Tue Oct 29 10:13:12 1996 Received: from thebe by elara via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) id KAA26004; Tue, 29 Oct 1996 10:13:06 -0600 Received: by thebe (951211.SGI.8.6.12.PATCH1042) id KAA02259; Tue, 29 Oct 1996 10:12:39 -0600 Date: Tue, 29 Oct 1996 10:12:37 -0600 (CST) From: David Larson Sender: David Larson Reply-To: David Larson Subject: Re: CCL:copy of screen view with SYBYL software To: Leon Dupont cc: chemistry@www.ccl.net In-Reply-To: <1.5.4.16.19961029142819.1e372cfc@pop3.mailst.ulg.ac.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I have written a macro 'image.spl' which captures images from Sybyl running on an Silicon Graphics workstation, writes them out to image files. http://www.tripos.com/services/spl_archive/image.spl image.spl will write out the following file formats: SGI RGB, GIF, PICT, TIFF, JPEG, ALIAS, TARGA, & Postscript If Postscript output is selected, a print command may be supplied by the user to direct output to the printer of choice. e.g. lpr -Pphaser PLEASE NOTE: This macro will run ONLY on Silicon Graphics workstations which have the necessary utiltities. I hope you find this useful. Please let me know if you have any questions. Best regards, David ---------------------------------------------------------------------------- David Larson Phone: 314 647 1099 Tripos Customer Support FAX: 314 647 9241 1699 S. Hanley Road WWW: http://www.tripos.com St. Louis, MO 63144 Email: dlarson@tripos.com ---------------------------------------------------------------------------- On Tue, 29 Oct 1996, Leon Dupont wrote: > Dear netters, > I am using the SYBYL software on a Silicon Graphics Indigo. > How could I get an exact printed copy of the screen view? > Postscript output included in Sybyl transforms the original view which > is seen on the screen. > Thank you. > L. Dupont > ____________________________________________________________________ > Dupont L=E9on | e-mail: Leon.Dupont@ulg.ac.be > Unit=E9 de Cristallographie | tel.: +32-4-366.37.62 > Institut de Physique Bat. B5 | fax: +32-4-366.23.55 > Universit=E9 de Li=E8ge au Sart-Tilman | > B 4000 LIEGE (Belgium) | http://www.ulg.ac.be/physexpe/crist/ > ____________________________________________________________________ > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Leon.Dupont@ulg.ac.be > -- Original Sender From: Address: Leon.Dupont@ulg.ac.be > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From blf2v@server1.mail.virginia.edu Tue Oct 29 12:32:50 1996 Received: from virginia.edu for blf2v@server1.mail.virginia.edu by www.ccl.net (8.8.0/950822.1) id MAA29889; Tue, 29 Oct 1996 12:23:02 -0500 (EST) Received: from server1.mail.virginia.edu by mail.virginia.edu id ab12662; 29 Oct 96 12:21 EST Received: from keller.Virginia.EDU (bootp-32-115.bootp.Virginia.EDU [128.143.32.115]) by server1.mail.virginia.edu (8.7.6/8.6.6) with SMTP id MAA26586 for ; Tue, 29 Oct 1996 12:21:29 -0500 (EST) From: "Barry L. Farmer" Sender: blf2v@server1.mail.virginia.edu To: CHEMISTRY@www.ccl.net Subject: postdoc position Message-ID: Date: Tue, 29 Oct 1996 12:21:34 -0500 () Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I have an IMMEDIATE OPENING for a postdoctoral research associate in computational chemistry. Experience in molecular mechanics and dynamics, and quantum mechanics (semiempirical methods) are required. Experience with CHARMM is also required. Experience with commercial software packages such as Quanta, Cerius-2, Spartan, Insight/Discover, and/or Sybyl will be useful. The position is part of an SBIR Phase II project which will involve both application of existing computational methods and participation in the development of new methods - in collaboration with a commercial software developer. The initial appointment will be for one year. One additional year is possible. Please send resume, list of publications, and names/addresses of references to: Barry L. Farmer, Department of Materials Science and Engineering, Thornton Hall, University of Virginia, Charlottesville, VA 22903-2442 Phone: 804-924-0605; Fax: 804-982-5660; Email: farmer@virginia.edu =========================================== Barry L. Farmer Dept. of Materials Science and Engr. Thornton Hall, University of Virginia Charlottesville, VA 22903-2442 Voice (804) 924-0605; Fax (804) 982-5660 farmer@virginia.edu From tevelde@chem.vu.nl Tue Oct 29 12:45:48 1996 Received: from gallium.chem.vu.nl for tevelde@chem.vu.nl by www.ccl.net (8.8.0/950822.1) id LAA29570; Tue, 29 Oct 1996 11:38:26 -0500 (EST) Received: from thallium.chem.vu.nl by gallium.chem.vu.nl (5.64/AUX-3.1.1) id AA16599; Tue, 29 Oct 96 17:38:22 MET Message-Id: <9610291638.AA16599@gallium.chem.vu.nl> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: binary Date: Tue, 29 Oct 1996 17:38:29 +0100 To: CHEMISTRY@www.ccl.net From: tevelde@chem.vu.nl (Bert te Velde) Subject: ADF Dear all, This is primarily a call upon all users of ADF who have NOT obtained a license directly from SCM or the Theoretical Chemistry Department of the Vrije Universiteit in Amsterdam. We wish to update our knowledge of the ADF user-base so as to be better able to enquire about research fields, technical issues, development and improvement preferences, etc. Therefore, we kindly ask you two minutes of your time to answer the questions below and send your answers to: adf@chem.vu.nl Please feel free to add any comments or suggestions you may have, also when not directly related to the questions. 1. would you like to be included in mailing lists to receive information about new releases or developments of ADF? 2. what is your affiliation type (industry, government research, academic, ...)? 3. what kind of platforms are you using ADF on? (eg: workstation, computers at SuperComputerCentre, parallel workstation clusters, mainframes, ...)? 4. Could you indicate the general application area / research field you are using ADF for? 5. when you have problems with understanding results or using the code, where do you go for help? (figure out yourself, someone else at your institute, the license provider (please indicate which), ....) Are you usually satisfied with how that works out? 6. how do you perceive the available documentation in general (not detailed enough, way too extended, ...)? Any details in your answer are appreciated. 7. do you use ADF primarily on its own or rather in conjunction with other chemistry codes (modelling, ab initio, semi-empirical, ...)? If the latter, could you indicate what for your research ADF's position is within the pack of programs you're using? 8. what are in your experience ADF's weakest points? What type of improvements / developments would be welcomed most in the context of your research? thanks for your attention, ---------------------------------------------------------------------------- Bert te Velde SCIENTIFIC COMPUTING & MODELLING phone: +31-20 44 47625 Chemistry Department, Vrije Universiteit fax +31-20-44 47643 De Boelelaan 1083; 1081 HV Amsterdam e-mail: tevelde@chem.vu.nl The Netherlands ---------------------------------------------------------------------------- From gmercier@mail.med.upenn.edu Tue Oct 29 13:32:50 1996 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.0/950822.1) id MAA29954; Tue, 29 Oct 1996 12:33:17 -0500 (EST) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.6.12/8.6.12) id MAA18615 for CHEMISTRY@www.ccl.net; Tue, 29 Oct 1996 12:33:18 -0500 From: "Gustavo A. Mercier Jr" Message-Id: <199610291733.MAA18615@mail.med.upenn.edu> Subject: MD/NVE. E/T fluctuations. What's too much? To: CHEMISTRY@www.ccl.net Date: Tue, 29 Oct 1996 12:33:18 -0500 (EST) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi, CCLer's I am running some MD simulations (a biorganic solute in H2O) using amber and need some guidance. What is too much of an energy fluctuation when running an NVE ensemble? The temperature is not fixed but targeted to 300K. How much leeway is reasonable in the fluctuations of the temperature and deviations between the mean temperature and the target temperature? In running simple Leonnard-Jones potentials, people take 1 in 10^4 as a reasonable fluctuation in the energy. The amber potential is more complex. Is 1 in 10^2 reasonable? Obviously the answer may depend on what I intend to do with the simulation. I am interested in the frequency spectrum of the atomic motions of the solute and some radial distribution functions. The goal is to generate friction coefficients and potentials of mean force for the atoms in the solute. Thanks for your kind reply. I will summarize to the net if there is enough interest. Gus Mercier, Jr. Univ. of Pennsylvania gmercier@mail.med.upenn.edu From martebr2@ussu.ciba.com Tue Oct 29 14:32:51 1996 Received: from pharma.ussu.Ciba.Com for martebr2@ussu.ciba.com by www.ccl.net (8.8.0/950822.1) id NAA00495; Tue, 29 Oct 1996 13:41:41 -0500 (EST) Received: by pharma.ussu.Ciba.Com (5.65/DEC-Ultrix/4.3) id AA11492; Tue, 29 Oct 1996 13:45:17 -0500 Sender: martebr1@ussu.Ciba.Com Message-Id: <32764E94.2F1C@ussu.ciba.com> Date: Tue, 29 Oct 1996 13:36:04 -0500 From: Bryan Marten X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Q:"linear" map to RGB for RasMol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, What is a (simple?) function to map a linear distribution of points to a ROYGBIV spectrum of colors expressed as RGB values? Stated more concretely: I have a distribution of data values which I would like to display graphically as continuous gradations in color where the color map ranges from red to blue/violet. These colors must be expressed as a set of RGB values ( 0 <= R,G,B <= 255 ). In other words, given a data value V, what are the values of R(V), G(V), and B(V) such that for V=-max you get "red" while for V=+max you get "blue/violet" and in between you get something resembling a rainbow? And a rainbow which appears to be a nice linear mapping to the human eye so that, if possible, one has a sense that "That color is 1/3 of the way >from red to blue so V must be about -17." I ask because I am attempting to modify my personal X/Unix copy of RasMol (obtained from http://www.umass.edu/microbio/rasmol) so that RasMol will use a continuous color distribution, instead of a coarse set of 8 colors, when it maps the molecular electrostatic potential to colors on a dotted van der Waals surface. Being color-theory impaired, I do not know of a good mapping as one finds in the program Grasp, among others. I understand that there are as many ways to map potential to color as there are known mathematical functions but something Grasp-like or in some sense perceived as "proportionally spaced" to the human eye would be great. I'll summarize and post the finished subroutine if there is interest, if the subroutine works, and if no one can point out licensing violations in doing so. Thanks in advance, -- Bryan Marten Ciba Pharmaceuticals martebr2@ussu.ciba.com From felllm@mcmail.cis.mcmaster.ca Tue Oct 29 15:32:53 1996 Received: from mcmail.CIS.McMaster.CA for felllm@mcmail.cis.mcmaster.ca by www.ccl.net (8.8.0/950822.1) id PAA01421; Tue, 29 Oct 1996 15:28:37 -0500 (EST) Received: from loki ([130.113.108.136]) by mcmail.CIS.McMaster.CA (8.7.1/8.7.1) with SMTP id PAA12802 for ; Tue, 29 Oct 1996 15:28:31 -0500 (EST) Date: Tue, 29 Oct 1996 15:28:31 -0500 (EST) Message-Id: <199610292028.PAA12802@mcmail.CIS.McMaster.CA> X-Sender: felllm@mcmail.cis.mcmaster.ca X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: "Lorne M. Fell" Subject: G: RO-MP2 possible? A quick question to the CCLers: Can G94 perform a ROMP2 type calculation? If so what does the program need to perform this calculation? I keep getting a file I/O error type error. Thanks in advance, Lorne Lorne M. Fell Department of Chemistry McMaster University email: felllm@mcmail.cis.mcmaster.ca