From ccl@www.ccl.net Mon Feb 2 13:09:23 1998 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA11216; Mon, 2 Feb 1998 12:50:40 -0500 (EST) Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by bedrock.ccl.net (8.8.6/8.8.6/OSC 1.0) with ESMTP id MAA14620 for ; Mon, 2 Feb 1998 12:50:36 -0500 (EST) Received: from wotan.duch.udel.edu (wotan.duch.udel.edu [128.175.54.25]) by copland.udel.edu (8.8.8/8.8.8) with SMTP id MAA04813 for <@brahms.udel.edu:chemistry@ccl.net>; Mon, 2 Feb 1998 12:50:38 -0500 (EST) Received: by wotan.duch.udel.edu (951211.SGI.8.6.12.PATCH1502/951211.SGI) id MAA03905; Mon, 2 Feb 1998 12:44:56 -0500 Date: Mon, 2 Feb 1998 12:44:55 -0500 (EST) From: Steve Bennett To: CCL Users Subject: Compiling Viewmol Message-ID: I am trying to compile the source for Viewmol 2.1 and am having trouble with link step. The error I am getting is: /bin/sh getmachine viewmol cc -o viewmol annotate.o basisform.o bondorder.o calcmo.o coledit.o cylinder.o distort.o draw.o drawel.o drawform.o drawop.o drawsp.o ellipse.o feedback.o fileselect.o getmem.o getrc.o hardcopy.o hpgl.o inert.o init.o input.o insint.o intern.o makemenu.o maketics.o manual.o marcub.o matrix.o messgb.o mkconn.o mo.o mkunitc.o moform.o mouseaction.o mousecb.o normod.o optiform.o osname.o postscript.o printform.o ray.o raytracer.o redraw.o resource.o runprog.o save.o saveform.o specform.o viewmol.o waveform.o window.o xfont.o zoom.o -L/usr/local/lib -lGLw -lGLU -lGL -lXm -lXt -lX11 -ltiff -lm ld: Unresolved: __eprintf *** Error code 1 (bu21) I am using IRIX 4600/5.3. Any suggestions would be appreciated. Steven D. Bennett University of Delaware Department of Chemistry 304A Drake Hall (302) 831-8720 sbennett@wotan.duch.udel.edu (302) 737-8485 http://udel.edu/~sbennett/steves.html "Scepticism is the chastity of the intellect, and it is shameful to surrender it too soon or to the first comer: there is nobility in preserving it cooly and proudly through long youth, until at last, in the ripeness of instinct and discretion, it can be safely exchanged for fidelity and happiness." George Santayana Scepticism and Animal Faith, IX From elewars@alchemy.chem.utoronto.ca Tue Feb 3 12:09:35 1998 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id LAA17013; Tue, 3 Feb 1998 11:36:15 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA15864 for chemistry@www.ccl.net; Tue, 3 Feb 1998 11:36:14 -0500 (EST) Date: Tue, 3 Feb 1998 11:36:14 -0500 (EST) From: "E. Lewars" Message-Id: <199802031636.LAA15864@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: BENCHMARKS FOR G94W ON PENTIUMPRO Tuesday 1998 Feb 3 SOME BENCHMARKS FOR G94 ON A PENTIUM PRO Hello, Here is a comparison of cpu times for G94 jobs on the Dec AlphaServer (presumably with UNIX) and the Pentium Pro with Windows NT 4.0. The DEC times were reported in the Gaussian Inc. book "Exploring Chemistry with Electronic Structure Methods", 2nd ed., by J. B. Foresman and A. Frisch, 1996 [a guide to Gaussian 94]; they are for a DEC AlphaServer with 5 GB disk and 250 MB RAM. The Pentium times are for a PentiumPro with 2 GB scratch space alloted to gaussian and 128 MB RAM, running G94W v. 4.2 (the DEC version is presumably UNIX G94 for a couple years earlier). The designations 2_05a etc are those used in "Exploring Chemistry..." Short jobs (< 20 min on DEC) | Medium jobs (0.3 h--<2h on DEC) job Time, min | job Time, h DEC Pentium Ratio | DEC Pentium Ratio 2_05a 3.0 8.0 2.7 |2_06 0.74 1.5 2.0 2_05b 2.8 6.7 2.4 |3_05a 1.0 3.2 3.2 2_05c 2.8 3.5 1.3 |3_05b 1.8 4.4 2.4 4_04d 7.3 6.8 0.9 |e4_02d 0.34 0.57 1.7 4_04e 6.0 10.2 1.7 |4_05a 0.92 1.9 2.1 4_04f 17.6 47 2.7 |e5_02 0.71 1.4 2.0 e9_02 3.9 2.9 0.7 |5_02 1.2 2.5 2.1 5_03a 0.75 2.6 3.5 5_03b 1.2 3.7 3.1 e6_06 0.50 0.80 1.6 6_03x 0.90 2.5 2.8 6_04 0.58 1.5 2.6 6_06d 0.53 1.1 2.1 6_08 0.62 0.87 1.4 8_01c 0.70 1.3 1.9 Long jobs (>=2 h on DEC) job Time, h DEC Pentium Ratio 3_06b 11.2 36 3.2 4_05b 2.0 4.7 2.4 5_04 3.4 10.5 3.1 e6_04 3.6 9.2 2.6 6_03 5.8 18.0 3.1 6_07b 2.0 7.3 3.7 10_04c 4.5 11.7 2.6 10_05a 4.1 12.4 3.0 10_05b 4.0 12.5 3.1 ------------------------------------------------------- It's said that (1) the PentiumPro may be faster than the Pentium II for number crucnching (see CCL archives for recent discussion) and (2) Linux is faster than Windows NT (which in turn is better than W 95 for this kind of work) but is not an operating system for "the faint of heart" (quoting one contributor to the Net). [Does anyone know how much a DEC AlphaServer costs, and how it compares with, say, the popular SGI Indy or O2 in speed?] E. Lewars elewars@trentu.ca ============================================== From destack@unomaha.edu Tue Feb 3 14:09:35 1998 Received: from s-cwis.unomaha.edu for destack@unomaha.edu by www.ccl.net (8.8.3/950822.1) id NAA17616; Tue, 3 Feb 1998 13:36:12 -0500 (EST) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id MAA19605; Tue, 3 Feb 1998 12:32:13 -0600 (CST) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 3 Feb 98 12:36:14 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 3 Feb 98 12:35:48 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 3 Feb 98 12:35:46 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BD30A0.860F1D40@zinc.unomaha.edu>; Tue, 3 Feb 1998 12:37:43 -0600 Message-ID: <01BD30A0.860F1D40@zinc.unomaha.edu> From: "Douglas E. Stack" To: "'CCL'" , "'spartan'" Subject: Mixing enthalpies and Entropies Date: Tue, 3 Feb 1998 12:37:42 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear CCLers: I would appreciate input for the following thoughts. I have molecules = who's size prohibits geometry Opt and freq. calculations at the HF/6-31G = level. I've been getting geometries with PM3 semi-empirical, then = submitting the geometry to a single-point HF6-31G calculation for energy = data (enthaphy only, can't do freq. calc. on the PM3 geometry). For = some of these reactions (addition reactions A+B-->C) entropy changes = could be important so I'd like calculate deltG of the reaction not just = deltaH. =20 My question is, can I use energy data from the HF6-31G calculation for = my enthaphy terms (deltaH), and mix them with my entropy data obtain = from PM3 semi-empirical frequency calculations. Will the small = contributions from entropy matter? And because there smaller than = enthalpy, is there more room for error in the entropy terms?=20 Douglas E. Stack=09 Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu From belsky@indy.jh-inst.cas.cz Tue Feb 3 15:09:35 1998 Received: from indy.jh-inst.cas.cz for belsky@indy.jh-inst.cas.cz by www.ccl.net (8.8.3/950822.1) id PAA17918; Tue, 3 Feb 1998 15:01:45 -0500 (EST) Received: from localhost by indy.jh-inst.cas.cz via SMTP (940816.SGI.8.6.9/930416.SGI) for id VAA19230; Tue, 3 Feb 1998 21:01:46 +0100 Date: Tue, 3 Feb 1998 21:01:45 +0100 (CET) From: Petr Belsky To: chemistry@www.ccl.net Subject: neutral glycine in CHARMM ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, This is to ask how to build neutral glycine in CHARMM, it means NH2-CH2-COOH. We are working with CHARMM 23 and only zwitterion of glycine is present there. Many thanks in advance Petr Belsky belsky@indy.jh-inst.cas.cz