From g112976@iris.ufscar.br Wed Sep 21 21:59:18 1994 Received: from fpsp.fapesp.br for g112976@iris.ufscar.br by www.ccl.net (8.6.9/930601.1506) id VAA05678; Wed, 21 Sep 1994 21:58:52 -0400 Received: from power.ufscar.br (200.9.84.65) by fpsp.fapesp.br with PMDF#10108; Wed, 21 Sep 1994 20:19 BSC (-0300 C) Received: from iris.ufscar.br by power.ufscar.br via SMTP (931110.SGI/911001.SGI) for @fpsp.fapesp.br:CHEMISTRY@oscsunb.ccl.net id AA25988; Wed, 21 Sep 94 20:19:10 -0200 Received: by iris.ufscar.br (920110.SGI/911001.SGI) for @power.ufscar.br:CHEMISTRY@oscsunb.ccl.net id AA25588; Wed, 21 Sep 94 22:14:41 -0200 Date: Wed, 21 Sep 94 22:14:41 -0200 From: g112976@iris.ufscar.br (Augusto C. C. Neto) Subject: mopacING and plotting To: CHEMISTRY@oscsunb.ccl.net Message-id: <9409220014.AA25588@iris.ufscar.br> X-Envelope-to: CHEMISTRY@oscsunb.ccl.net Hi netters I'm working with mopac 5 and would like to plot in my SGI some outputs from this package, like : - energy reaction path - spin density - molecular electrostatic potential - molecular orbitals In what ftp sites could I find some programs that plot the informations said above ??? Please send the posible answers right to me. Thank you .... Augusto Cesar Universidade Federal de Sao Carlos Brazil From upolklan@savba.savba.sk Thu Sep 22 02:59:31 1994 Received: from nic.uakom.sk for upolklan@savba.savba.sk by www.ccl.net (8.6.9/930601.1506) id CAA08824; Thu, 22 Sep 1994 02:08:04 -0400 Received: from savba.savba.sk by nic.uakom.sk with SMTP id AA02520 (5.65c/IDA-1.4.4 for ); Thu, 22 Sep 1994 08:07:34 +0200 Received: by savba.savba.sk id AA27654 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 22 Sep 1994 08:09:02 +0200 From: Angela Kleinova Message-Id: <199409220609.AA27654@savba.savba.sk> Subject: C60-isopropyl rotational barrier To: chemistry@ccl.net Date: Thu, 22 Sep 1994 08:09:02 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL5] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 6284 Dear netters, probably i'm blind, but i can't find error in this MOPAC input... (the total energies and heats of formations are wrong) thanX for any help ;-) cat << END_OF_MOPAC_INPUT UHF AM1 ITRY=999 NOXYZ SCFCRT=0.001 DOUBLET HYPERFINE SYMMETRY BONDS PULAY + PL NOINTER C60-CH(CH3)2 RADICAL: GEOMETRY PARTIALLY OPTIMIZED FOR R-C ATOMS BY HYPERCHEM MOPAC7 BREAKS R-C BOND !!! ISOPROPYL GROUP IS SYMMETRIC TO PENTAGON. ROTATE ! C C 2.48994 0 1 C 1.53918 0 72.05315 0 1 2 C 1.53928 0 71.98922 0 0.09087 0 2 1 3 C 4.41948 0 83.85482 0 -138.43797 0 1 2 3 C 1.54042 0 96.10179 0 0.08544 0 5 1 2 C 1.53936 0 24.10731 0 -121.19206 0 5 1 2 C 1.53902 0 108.04051 0 -21.62106 0 6 5 1 C 1.54098 0 120.05704 0 120.95932 0 6 5 1 C 1.54104 0 112.79691 0 126.26726 0 5 1 2 C 1.53921 0 119.94681 0 -112.24012 0 10 5 1 C 1.53917 0 119.90222 0 -0.16616 0 9 6 5 C 1.54109 0 120.08505 0 142.75043 0 8 6 5 C 1.54114 0 120.06167 0 -79.33024 0 7 5 1 C 1.53899 0 119.98846 0 -138.30213 0 13 8 6 C 1.53956 0 120.00037 0 138.39291 0 14 7 5 C 1.54087 0 119.87103 0 -142.43404 0 3 1 2 C 1.53902 0 119.98816 0 138.04360 0 17 3 1 C 1.54133 0 119.95723 0 142.61772 0 4 2 1 C 1.53931 0 119.89603 0 -138.01925 0 19 4 2 C 2.66413 0 130.27125 0 119.11534 0 20 19 4 C 1.53981 0 90.07151 0 -131.12871 0 21 20 19 C 1.53922 0 107.90444 0 142.46791 0 22 21 20 C 1.53904 0 139.12460 0 -12.66142 0 21 20 19 C 1.53927 0 108.01013 0 -142.75457 0 12 9 6 C 1.53947 0 107.96550 0 142.80718 0 11 10 5 C 1.54077 0 119.86505 0 142.60890 0 25 12 9 C 2.49131 0 144.03085 0 -100.70253 0 27 25 12 C 1.54017 0 120.05224 0 0.18763 0 27 25 12 C 1.53927 0 119.93465 0 -137.91183 0 27 25 12 C 1.53895 0 107.98916 0 -142.62070 0 29 27 25 C 1.53935 0 108.03196 0 0.24565 0 23 22 21 C 1.53920 0 36.01737 0 179.71483 0 1 2 3 C 1.54090 0 120.13601 0 -0.25435 0 30 27 25 C 1.53914 0 119.90876 0 138.27933 0 34 30 27 C 1.54132 0 120.06119 0 -142.55061 0 23 22 21 C 1.53976 0 120.00811 0 138.37555 0 36 23 22 C 1.53955 0 108.01504 0 -0.11265 0 26 11 10 C 1.53988 0 107.98065 0 0.26269 0 25 12 9 C 2.49014 0 144.11738 0 37.02607 0 17 3 1 C 2.49018 0 71.99883 0 142.54154 0 20 19 4 C 1.53894 0 72.05129 0 -0.05198 0 41 20 19 C 1.53905 0 36.03821 0 -63.33057 0 40 17 3 C 1.53923 0 108.03638 0 -0.24957 0 39 25 12 C 1.53895 0 107.98845 0 -142.65164 0 16 14 7 C 1.53915 0 120.02435 0 0.11906 0 36 23 22 C 1.53946 0 108.01053 0 0.15078 0 38 26 11 C 1.53912 0 120.05048 0 0.08157 0 14 7 5 C 1.53963 0 108.09422 0 -142.57721 0 35 34 30 C 1.53915 0 107.99821 0 -142.61663 0 37 36 23 C 1.53923 0 119.94225 0 0.34985 0 34 30 27 C 1.53969 0 108.00914 0 142.60962 0 15 13 8 C 1.53912 0 120.03340 0 -0.05444 0 13 8 6 C 1.53997 0 108.02015 0 -0.15395 0 50 37 36 C 1.53993 0 108.04042 0 -0.16323 0 45 16 14 C 1.53984 0 108.00408 0 0.15427 0 52 15 13 C 1.53967 0 107.98495 0 142.43913 0 51 34 30 C 1.53931 0 107.95129 0 -142.84649 0 18 17 3 C 1.53960 0 108.05901 0 142.79431 0 20 19 4 C 1.50509 0 107.97448 0 0.00000 0 8 6 5 C 1.50001 0 103.17339 0 -115.73466 -1 60 8 6 C 1.54104 0 109.00040 0 117.04235 0 61 60 8 C 1.54099 0 108.99995 0 -2.95669 0 61 60 8 H 0.99996 0 108.99706 0 -122.95690 0 61 60 8 H 1.09000 0 108.99832 0 68.42071 0 63 61 60 H 1.09000 0 109.93817 0 -51.00122 0 63 61 60 H 1.09000 0 109.93340 0 -172.16441 0 63 61 60 H 1.09000 0 109.00089 0 59.87355 0 62 61 60 H 1.09000 0 109.93765 0 -59.54544 0 62 61 60 H 1.09000 0 109.93666 0 179.29524 0 62 61 60 62 1 63 62 2 63 65 1 66, 67, 68, 69, 70 65 2 66, 67, 68, 69, 70 62 7 64 62 11 63 67 7 66 67 11 65 69 7 68 69 11 70 5 125 END_OF_MOPAC_INPUT +-----------------------------------------------------------------------+ + Dr. Angela Kleinova + + Polymer Institute + + Slovak Academy of Sciences Tel: ++42 +7 378 2252 + + Dubravska cesta 9, 842 28 Bratislava Fax: ++42 +7 821 685 + + Slovak Republic E-mail: upolklan@savba.sk + + EUROPE + +-----------------------------------------------------------------------+ ,,, (o o) +-----------------------------oOO--(_)--OOo-----------------------------+ + And all this science I don't understand, it's just my work for 5 days + + a week ... +-----------------------------------------------------------------------+ From CHMORA@LSUVAX.SNCC.LSU.EDU Thu Sep 22 03:59:26 1994 Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by www.ccl.net (8.6.9/930601.1506) id DAA09563; Thu, 22 Sep 1994 03:39:16 -0400 Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426) id <01HHEATRZ7YO8X1DA3@LSUVAX.SNCC.LSU.EDU>; Thu, 22 Sep 1994 02:40:59 CST Date: Thu, 22 Sep 1994 02:40:59 -0600 (CST) From: CHMORA@LSUVAX.SNCC.LSU.EDU Subject: Mopac for OS/2 ? To: chemistry@ccl.net Message-id: <01HHEATRZHMA8X1DA3@LSUVAX.SNCC.LSU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi Netters, Does anyone know if MOPAC is available for OS/2 ? Thanks. Guillermo A. Morales Chemistry Department Louisiana State University Baton Rouge, LA 70803-1804 Phone: (voice) 504/388-2706 (fax) 504/388-3458 E-mail: CHMORA@SN01.SNCC.LSU.EDU From mulcrone@luigistoaster.pds.charlotte.nc.us Thu Sep 22 07:59:28 1994 Received: from luigistoaster.pds.charlotte.nc.us for mulcrone@luigistoaster.pds.charlotte.nc.us by www.ccl.net (8.6.9/930601.1506) id HAA10624; Thu, 22 Sep 1994 07:37:26 -0400 Received: by luigistoaster.pds.charlotte.nc.us (5.65/DEC-Ultrix/4.3) id AA11992; Thu, 22 Sep 1994 07:37:26 -0400 Date: Thu, 22 Sep 1994 07:37:26 -0400 From: mulcrone@luigistoaster.pds.charlotte.nc.us (The Man) Message-Id: <9409221137.AA11992@luigistoaster.pds.charlotte.nc.us> To: CHEMISTRY@ccl.net Subject: cesium Hello again, My name is Daniel Mulcrone, a tenth grader at Providence Day School in Charlotte, North Carolina. Recently, I mailed the list about "my favorite element," scandium. The responses I got were very helpful. Thank you to all who sent responses! The information that I got off the internet stunned both me and my chemistry teacher and eventually more people became interested in the listserv. A friend of mine asked me if I would get some info on her element, cesium. Since we attend a private school, good resources are sometimes scarce. If ANYONE has any information out there about cesium, I would appreciate it. Again, thanks for all of the great info on scandium, and I look forward to learning a little about cesium. Thanks in advance! Daniel Mulcrone ***Please send all responses to: mulcrone@luigistoaster.pds.charlotte.nc.us Thanks! From Patrick.Bultinck@rug.ac.be Thu Sep 22 09:59:33 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id JAA12022; Thu, 22 Sep 1994 09:35:32 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA21197 (5.67b/IDA-1.5 for ); Thu, 22 Sep 1994 15:34:45 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA19222; Thu, 22 Sep 1994 15:35:31 +0200 Date: Thu, 22 Sep 1994 15:35:30 +0200 (MET DST) From: Patrick Bultinck Subject: Making ECP's To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 512 Dear Netters, I would like to know if there are programs that would allow me to make ECP's (Effective Core Potentials) (relativistic as well as non-relativistic) for alkaline and alkaline-earth metal IONS. Please if you know of such programs let me know, alternatively references to articles which give results on ECP's for the requested ions are also gladly accepted ! As always, if there is enough interest, I will post a summary ! Thank you very much, Patrick Bultinck, University of Ghent (Belgium) From UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca Thu Sep 22 10:08:27 1994 Received: from BANEE.rmc.ca for UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca by www.ccl.net (8.6.9/930601.1506) id JAA12318; Thu, 22 Sep 1994 09:54:48 -0400 From: Message-Id: <199409221354.JAA12318@www.ccl.net> Received: by BANEE.rmc.ca with VINES ; Thu, 22 Sep 94 10:14:36 EDT Date: Thu, 22 Sep 94 09:10:31 EDT Subject: md, equilibriation times and vibrations To: chemistry@ccl.net I've encountered a problem with MD that experienced modellers may be able to put my mind to rest about. Taking an isolated molecule (a mere 28 atoms) which had been loosely geometry optimized, I turned it loose in a molecular dynamics simulation using PM3 and monitored a few bond torsions and the potential energy. (1 fs time step and .1ps bath relaxation). The potential energy slowly drifted downward and after 20ps seemed to be assymptotically approaching a binding energy of -2542 kcal/mole. During this time the torsions which I was observing noticeably damped down substantially. Afterwards I optimized the molecule, getting an energy of about -2546 kcal/mole and started a new md run with the new structure with a heating period of 1 ps to 300C. The potential energy leaped up about 25 kcal/mole which seems about right (28 * 3/2 *(RT=.6kcal/mole)). The potential energy is slowly settling back down and presumably will approach -2542 kcal/mole again. Observing the damping out of the torsions and the small change in the mean potential energy (4kcal/mole) between the minimized structure and the equilibrium one, has lead to worry about where are the zero point vibrations. When the simulations are started the atoms are given randomn directions which basically excites all sorts of modes. As the molecule deexcites and the bath carts off the excess energy all the bond vibrations (bends, stretches and torsions) seem to be disappearing so that one is left with a molecule travelling through space and spinning but that's all. I dusted off my trusty old QM textbook and looked up 1-d harmonic oscillators. It pointed out that zero point energy (that 1/2h(nu)) is a quantum mechanical effect arising from the non-commutation of the positon and momentum operators (i.e. the Heisenberg uncertainty principle raises its ugly head). Now in a computer simulation of a molecule there is no such problem about commutation. I can know both the position and momentum of the nuclei to arbitrary accuracy. Does this mean that if I wait long enough the vibrations will all freeze out completely and I'll be left with a spinning molecule careening through space. One might also point out that it will be spinning and careening far too fast since the bath will make sure the overall kinetic energy, alot of which should be tied up in vibrations, is correct. Obviously in a liquid, inter-molecular interactions will cause randomization of some sort and pump energy back into vibrational modes. However, the whole thing leaves me a little concerned about these kind of calculations. Can someone out there reassure me? Ross Underhill underhil@me2.rmc.ca From vasz@bif.creighton.edu Thu Sep 22 10:59:32 1994 Received: from bif.creighton.edu for vasz@bif.creighton.edu by www.ccl.net (8.6.9/930601.1506) id KAA13176; Thu, 22 Sep 1994 10:27:55 -0400 Received: by bif.creighton.edu (920330.SGI/911001.SGI) for chemistry@ccl.net id AA05740; Thu, 22 Sep 94 09:13:48 -0500 Date: Thu, 22 Sep 94 09:13:48 -0500 From: vasz@bif.creighton.edu (Sandor Lovas) Message-Id: <9409221413.AA05740@bif.creighton.edu> To: chemistry@ccl.net Subject: Re.CCL:Mopac for OS/2 ? Guillermo A. Morales asked about availibility of MOPAC for OS/2. I converted MOPAC93 for OS/2 2.1 using Microway's NDP860 fortran compiler Ver.4.1 with a little modification. In opposite to QCPE's QCMP130 this is a fully ported package and containing ESP calculation. Sandor Lovas Dept. Biomed. Sci. Creighton University Omaha, NE 68178 E-mail: vasz@bif.creighton.edu From HODGKINE@prince.mm.wyeth.com Thu Sep 22 11:00:47 1994 Received: from mail1 for HODGKINE@prince.mm.wyeth.com by www.ccl.net (8.6.9/930601.1506) id KAA12583; Thu, 22 Sep 1994 10:06:11 -0400 Received: from mr.wyeth.com by mail1.wyeth.com (PMDF V4.2-14 #5660) id <01HHEQJBY39C000U92@mail1.wyeth.com>; Thu, 22 Sep 1994 10:07:35 EST Received: with PMDF-MR; Thu, 22 Sep 1994 10:04:54 EST MR-Received: by mta PRIN1; Relayed; Thu, 22 Sep 1994 10:04:54 -0500 MR-Received: by mta MAIL1; Relayed; Thu, 22 Sep 1994 10:06:53 -0500 Disclose-recipients: prohibited Date: Thu, 22 Sep 1994 15:08:58 -0500 (EST) From: "Hodgkin, Ed" Subject: Summary - VDW Collapse To: "chemistry@ccl.net" Message-id: <01HHEQJRN4PC000U92@mr.wyeth.com> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT UA-content-id: Summary - VDW Collapse X400-MTS-identifier: [;45400122904991/226625@PRINCE] A1-type: MAIL Hop-count: 1 From: Hodgkin, Ed Date: Thu, Sep 22, 1994 3:08 PM Subject: Summary - VDW Collapse To: chemistry@ccl.net Dear CCL A summary of replies to my "VDW Collapse" question of 2nd Sept. I think you'll agree there are some excellent comments. Sorry about the delay and thanks to everyone who replied. PS. The replies seem to be listed in reverse order! Edward Hodgkin Wyeth Research (UK) hodgkine@prince.mm.wyeth.com Message for Hodgkin, Ed From: chemistry-request Date: Fri, Sep 2, 1994 2:29 pm Subject: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 31437120904991/454392@MAIL1 From: NAME: chemistry-request Author: NAME: bear To: NAME: chemistry Date : 2-SEP-1994 14:29:26.00 |> From: Hodgkin, Ed |> force fields favour 'folded' conformations |> From: David States |> most direct way to control for the self-association |> of peptide chains is to do a simulation that includes |> solvation explicitly... |> From: Jeff Nauss |>Is anything similar observed with AMBER... In my work with solvated DNA under AMBER dynamics with periodic boundary, water does NOT stop collapse. bear * UU UU SOARING BEAR * * UU UU Computer Aided Drug Design * * UU UU A University of Arizona, New Pharmacy 404 * * UUUU AAA Tucson, AZ 85721 602-626-6133 * * AA AA where the sun shines * * AAAAAAA * * AA AA e-mail:bear@ellington.pharm.arizona.edu * ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: bear Date: Fri, Sep 2, 1994 1:48 pm Subject: Re: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 93954120904991/454156@MAIL1 From: NAME: bear To: NAME: Hodgkin, Ed Date : 2-SEP-1994 13:48:51.00 "Van Der Waals Collapse", yes, what a great term. I've been observing and sometimes struggling with this with our DNA models for some time but never had such a good name for it. I have the feeling that it suggests further refinements in force fields are necessary. Restraints will prevent such a collapse but defeat the whole purpose of mechanics and dynamics. bear * UU UU SOARING BEAR * * UU UU Computer Aided Drug Design * * UU UU A University of Arizona, New Pharmacy 404 * * UUUU AAA Tucson, AZ 85721 602-626-6133 * * AA AA where the sun shines * * AAAAAAA * * AA AA e-mail:bear@ellington.pharm.arizona.edu * ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: chemistry-request Date: Fri, Sep 2, 1994 10:30 am Subject: CCL:collapsing water droplets To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 05722120904991/453892@MAIL1 From: NAME: chemistry-request Author: NAME: Heather Carlson To: NAME: chemistry Date : 2-SEP-1994 10:30:06.00 Just another word on simulated water droplets (spherical caps)... During a simulation of a 12 A radius cap, we observed the compression previously mentioned on the net. In order to obtain the same O-O radial distribution function in a periodic cell, we have to set the NPT ensemble to 1500 atm. I realize this isn't addressing the vdw collapse, but since droplet compression was mentioned, I figured it would be of interest since adding an extra factor of compressiomn would be counter-productive. Heather Carlson heather@ramana.chem.yale.edu ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: chemistry-request Date: Fri, Sep 2, 1994 8:31 am Subject: CCL:VDW collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 83720120904991/453730@MAIL1 From: NAME: chemistry-request Author: NAME: Rick Loncharich To: NAME: chemistry Date : 2-SEP-1994 08:31:15.00 |> From: Hodgkin, Ed |> |> It is well known that molecular mechanics force fields favour 'folded' |> conformations which derive stability from large Van Der Waals terms. |> One could coin the phrase "Van Der Waals Collapse" to describe this |> effect.... |> From: David States |> . . . The most direct way to |> control for the self-association of peptide chains is to do a |> simulation that includes solvation explicitly. Note that if you do |> this as a water droplet rather than a periodic box the internal |> pressure generated by surface tension is enormous so the system will |> still collapse some compared to physiologic conditions. Furthermore, as one increases the amount of water in a water droplet simulation from 0 to 4000 water molecules the size of the protein (measured by rgyr) increases to the X-ray radius of gyration. See recent articles by B.R. Brooks et. al. Rick Loncharich Eli Lilly and Company From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"chemistry@ccl.net") ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: chemistry-request Date: Fri, Sep 2, 1994 8:11 am Subject: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 61620120904991/453724@MAIL1 From: NAME: chemistry-request Author: NAME: nauss To: NAME: CHEMISTRY Date : 2-SEP-1994 08:11:17.00 >From: states@ibc.wustl.edu (David J. States) >|> From: Hodgkin, Ed >|> >|> It is well known that molecular mechanics force fields favour 'folded' >|> conformations which derive stability from large Van Der Waals terms. >|> One could coin the phrase "Van Der Waals Collapse" to describe this >|> effect.... > >From the earliest days of charmm development, this has been a concern. >Globular proteins simulated in vacuo shrink when "true" atomic radii >are used as the basis for nonbonded interaction parameters... >The most direct way to >control for the self-association of peptide chains is to do a >simulation that includes solvation explicitly. I observed this phenomenon when I was running CHARMM a couple years ago. However, it does not appear to be a major problem with Biosym's Discover using the CVFF forcefield. I emphasis the word major as I do observe some collapse of proteins and peptides but never to the extent that CHARMM produced. Anyone have any comments on the difference between the two forcefields and this "Van Der Waals Collapse?" Is anything similar observed with AMBER or GROMOS? Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC * **************************************************************************** ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: gregory Date: Fri, Sep 2, 1994 4:29 am Subject: Re: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 95610120904991/453716@MAIL1 From: NAME: gregory To: NAME: Hodgkin, Ed Date : 2-SEP-1994 04:29:28.00 There are basically two separate problems with atom-atomic energy calculations. One is for large molecules (proteins). Any estimations of intramolecular energy are just estimations. In other words, if you have an error of 0.0001% in estimation of every individual atom-atomic interaction (say, Ecalcd = 0.25 kcal/mol instead of the "real" 0.2500025 value), you will need about 1,000 atoms interacting with each other, to get an overall error of 100%. (O.K., there might be some compensatory effects; let us suggest 2,000 atoms.) This means that any energy estimations in large system would not give you a correct energy value. Therefore, any efforts spent on molecular mechanics calculations of proteins cannot, generaly speaking, reach their goals. Accordingly, you do not need to worry about the "vdW" collapse in this case. Small molecules (peptides) are different. Here you can count on your energies, at least you can safely pick out those inside some enrgy threshold (but do not think, that that with E = 1.5 kcal/mol is really better than that of 4.5 kcal/mol; considering the inevitable errors involved, they are equal). My experience with the ECEPP is that up to hexa/heptapeptide you will always have a large variety of folded/extended 3D structures among your low-energy (i.e., those with energies less than detlaE) conformers. Moreover, the averaging (of special sort) over these conformers will give you a good agreement with an experiment in solution. As to the conformers binding to receptors, all our models (proved by experiment) were folded conformers. However, if you follow the rule of keeping ALL low-energy conformers as possibilities, you will keep the extended conformers (like that of protease substrates) as well. In other words: you cannot solve the "vdW" collapse problem, but you can obtain the correct results by taking into account all (or as close to all as you can) low-energy conformers for your system. Good luck. Gregory Nikiforovich ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: Julian Tirado-Rives Date: Fri, Sep 2, 1994 8:38 am Subject: Re: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 64149020904991/453575@MAIL1 From: NAME: Julian Tirado-Rives To: NAME: HODGKINE Date : 2-SEP-1994 08:38:49.00 > > From: Hodgkin, Ed > Date: Fri, Sep 2, 1994 9:30 AM > Subject: Van Der Waals Collapse > To: chemistry@ccl.net > Dear All > > It is well known that molecular mechanics force fields favour 'folded' > conformations which derive stability from large Van Der Waals terms. One could > coin the phrase "Van Der Waals Collapse" to describe this effect. However I am > not aware of any published work which addresses this issue. Are there any > methods which compensate for the folding effect, thereby giving lower energies > for extended conformations which are probably more relevant for molecules in > solution or in binding sites. > > I'll summarize the replies, of course. > > Edward Hodgkin > Wyeth Research (UK) > E-mail: hodgkine@prince.mm.wyeth.com > Do you have any references for this "well known" fact? Given that there are published reports of unfolding proteins in solution I would be curious to know how was the unfeasibility of this simulation stablished. Thanks! --------------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: julian@matrix.chem.yale.edu | | New Haven, CT 06520-8107 | | --------------------------------------------------------------------- ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: theochem Date: Fri, Sep 2, 1994 8:52 am Subject: vdW collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 24558020904991/453481@MAIL1 From: NAME: theochem To: NAME: hodgkine Date : 2-SEP-1994 08:52:58.00 Ed: A real example of this situation occurred in our papers in Tetrahedron Letters in which we studied the conformations of Gellman's amides using the MacroModel AMBER force field. Our results overestimated the contribution of the seven-membered ring hydrogen bonded conformation relative to the 9 and 6 conformations. Clark Still then reparameterized AMBER and announced AMBER*, which included some new torsional terms to correct for this problem. Just shortly after we published our modeling results, Mike Whang-bo published a semiempirical study of the same systems and came to the same conclusions. So something in MOPAC/AM1 also lead to an overestimation of the 7-membered ring. This may be an artifact due to the use of gaussian functions in the semiempirical paramterization, but J. Stewart or A. Holder would be more appropriate sources of information on that. I do not have all my references handy because of my recent move to CTC, but my papers appeared in Tet. Letters 1991, 32, 3613-6 and 3617-20. Sam Gellman had a response in Tet. Letters late in the same year or early the next year; Still's paper (I believe that Quentin McDonald is the lead author) appeared at the end of 1991 or 1992 in TL as well. Whang-bo's work appeared in JACS early in 1992 (I believe). Doug -- Douglas A. Smith Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com !!!NEW!!! Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. and still: Douglas A. Smith voice: N/A Associate Professor fax: N/A Department of Chemistry email: dsmith@uoft02.utoledo.edu and Center for Drug Design and Development The University of Toledo Toledo, OH 43606-3390 +---------------------------------+---------------------------------+ | "The juvenile sea squirt wanders through the sea searching for | | a suitable rock or hunk of coral to cling to and make its home | | for life. For this task it has a rudimentary nervous system. | | When it finds its spot and takes root, it doesn't need its | | brain any more so it eats it. It's rather like getting tenure." | | --source unknown | +-------------------------------------------------------------------+ ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: chemistry-request Date: Fri, Sep 2, 1994 7:19 am Subject: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 84748020904991/453460@MAIL1 From: NAME: chemistry-request Author: NAME: states To: NAME: HODGKINE To: NAME: chemistry Date : 2-SEP-1994 07:19:12.00 |> From: Hodgkin, Ed |> |> It is well known that molecular mechanics force fields favour 'folded' |> conformations which derive stability from large Van Der Waals terms. |> One could coin the phrase "Van Der Waals Collapse" to describe this |> effect.... From the earliest days of charmm development, this has been a concern. Globular proteins simulated in vacuo shrink when "true" atomic radii are used as the basis for nonbonded interaction parameters. Swaminathan spent alot of time working on a compensating force term, but I don't know what became of the work. The most direct way to control for the self-association of peptide chains is to do a simulation that includes solvation explicitly. Note that if you do this as a water droplet rather than a periodic box the internal pressure generated by surface tension is enormous so the system will still collapse some compared to physiologic conditions. David States ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: MARYJO Date: Fri, Sep 2, 1994 7:39 am Subject: Re: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 92047020904991/453316@MAIL1 From: NAME: MARYJO To: NAME: HODGKINE Date : 2-SEP-1994 07:39:52.00 Hello Edward. It is my opinion that van der Waals collapse should be observed if large molecules can be released to the gas phase and probed. I believe that the unfair favoritism of folded structures in the condensed phase is a simple consequence of inadequate treatment of intermolecular forces, in many cases. The often excluded molecule-solvent and intermolecular forces between neighboring molecules will compete with intramolecular forces. Many standard modelling software packages do not automatically incorporate these competing forces, and thus folded structures prevail. Mary Jo Ondrechen ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ Message for Hodgkin, Ed From: chemistry-request Date: Fri, Sep 2, 1994 9:30 am Subject: CCL:Van Der Waals Collapse To: Hodgkin, Ed File(s): Attach.Txt1 Regarding Message ID : 00216020904991/453268@MAIL1 From: NAME: chemistry-request Author: NAME: Hodgkin, Ed To: NAME: chemistry@ccl.net Date : 2-SEP-1994 09:30:15.00 From: Hodgkin, Ed Date: Fri, Sep 2, 1994 9:30 AM Subject: Van Der Waals Collapse To: chemistry@ccl.net Dear All It is well known that molecular mechanics force fields favour 'folded' conformations which derive stability from large Van Der Waals terms. One could coin the phrase "Van Der Waals Collapse" to describe this effect. However I am not aware of any published work which addresses this issue. Are there any methods which compensate for the folding effect, thereby giving lower energies for extended conformations which are probably more relevant for molecules in solution or in binding sites. I'll summarize the replies, of course. Edward Hodgkin Wyeth Research (UK) E-mail: hodgkine@prince.mm.wyeth.com ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV ************************************************ Text attachment found and added as enclosure ************************************************ ============================================================ From topper@cooper.edu Thu Sep 22 11:59:42 1994 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.6.9/930601.1506) id LAA14639; Thu, 22 Sep 1994 11:11:38 -0400 Received: by magnum.cooper.edu with UUCP id AA09606 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Thu, 22 Sep 1994 11:11:45 -0400 Date: Thu, 22 Sep 1994 11:11:45 -0400 From: Robert_Topper Message-Id: <199409221511.AA09606@magnum.cooper.edu> To: CHEMISTRY@ccl.net Subject: Subject: HS Sci Ed & NEWTON Content-Length: 3758 Since some high-school students seem to be tuning into this space, I felt that it might be useful to tell everyone about NEWTON. NEWTON is a public BBS maintained by Argonne National Laboratory's Division of Educational Programs. Although not affiliated with Argonne, I have been working with them as a volunteer for several years now. NEWTON (newton.dep.anl.gov) has a series of moderated sections called "Ask-A-Scientist." Arranged by topic (chemistry, physics, math, etc.), students in grades K-12 (literally) and their teachers can post questions on different topics, to be answered by volunteer scientists who have been "cleared" by Argonne. Any qualified scientist is welcome to volunteer to answer questions on NEWTON, and any student (qualified or not) is welcome to "drop in" and ask questions. So I hope that Dan Mulcrone and his friends and teachers will feel free to telnet to NEWTON at newton.dep.anl.gov . That said; I realize that Dan and his friends are getting a lot of useful information without having to hit the library by asking about their assigned elements on the CCL...but is this a good thing? Last year, no less than 20 students (all in the same class) logged into NEWTON asking for enough information to write 3-page reports on their assigned elements...tungsten, chlorine, cadmium, etc.... In the end, we (the volunteers working the chemistry section) determined that we could not, and would not, honor such requests. I wonder whether just handing students information which they could find out by hitting local libraries, newspapers, college libraries and other resources (interlibrary loan is the small-town librarian's friend) is really helping them. After all, part of a scientific education is learning how to use available library resources effectively. I'm sympathetic to the students' frustration with their own school's library....I grew up in small towns in North Carolina and in western Colorado. But the fact is that there are other local resources they can use if they just ask. When in high school, I had a paper to write on botanical remedies. I hit the school and local public libraries, as well as the library at the local 2-year college. I went to local hospitals (many of which have journal collections), and interviewed pharmacists, doctors, and health-food store owners..just generally hit the pavement. Ultimately I came out with a pretty good paper. Certainly, the INTERNET is a vast resource and it's good for students to learn how to use it to do research...but ultimately I feel that what a student is asking for in this situation is for a lot of people to each do a little work for them so that they have little left to do for themselves (except write it up). And is that a good thing? Well, each must decide. But remember; when citing sources in a published scientific paper, one usually has to be a little more specific about where information comes from than "someone sent me an email message." Best to all, especially you future chemists out there - rqt ************************************************************************ Prof. Robert Q. Topper internet: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 Cooper Square subway: take the N/R to 8th/NYU New York, NY 10003 USA or the 6 to Astor Place The Cooper Union for the Advancement of Science and Art, established by Peter Cooper in 1859, is a private institution of higher learning where all students receive full-tuition scholarships. ************************************************************************ From y_zheng@ccmail.pnl.gov Thu Sep 22 12:59:34 1994 Received: from pnl.gov for y_zheng@ccmail.pnl.gov by www.ccl.net (8.6.9/930601.1506) id MAA15927; Thu, 22 Sep 1994 12:28:30 -0400 Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.2-15 #4032) id <01HHEOZKPVOW008K6G@pnl.gov>; Thu, 22 Sep 1994 09:23:03 PDT Date: Thu, 22 Sep 1994 08:54 -0700 (PDT) From: y_zheng@ccmail.pnl.gov Subject: Parameters for nickel and iron-sulfur clusters To: chemistry@ccl.net Message-id: <01HHEOZLC48I008K6G@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, I am looking for force field parameters for Ni and iron-sulfur clusters. Any help will be appreciated. Thanks. Yajun From ma_thompson@ccmail.pnl.gov Thu Sep 22 13:03:27 1994 Received: from pnl.gov for ma_thompson@ccmail.pnl.gov by www.ccl.net (8.6.9/930601.1506) id MAA15761; Thu, 22 Sep 1994 12:16:38 -0400 Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.2-15 #4032) id <01HHEOKEW7KG008K6G@pnl.gov>; Thu, 22 Sep 1994 09:10:50 PDT Date: Thu, 22 Sep 1994 09:07 -0700 (PDT) From: ma_thompson@ccmail.pnl.gov Subject: Periodic Systems & Commercial Codes To: chemistry@ccl.net Message-id: <01HHEOKG7D3M008K6G@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT I would like to hear about any commercial codes that can do the following: 1). Solvate a molecule in an arbitrary box (for the purpose of setting up a periodic system). 2). Able to do #1 with any solvent molecule I specify. 3). Has an openly defined molecular dynamics trajectory file format that to which I can convert my MD trajectories, for the purpose of analysis and visualization. Also, must be able animate MD trajectories and do some "real" analysis, like rdf, average structural properties, etc. 4). Is able to do the above on systems as large as 40K atoms. I know that Insight can do this. How about products like CAChe, HyperChem, or any others out there. I have no great desire to run MD calculations with the computational codes that come with these packages. Rather, I wish to interface capabilities 1-3 with our own MD codes. From ross@cgl.ucsf.EDU Thu Sep 22 15:59:36 1994 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.9/930601.1506) id PAA18816; Thu, 22 Sep 1994 15:16:29 -0400 Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.9/GSC4.24) id MAA29075 for chemistry@ccl.net; Thu, 22 Sep 1994 12:16:27 -0700 Date: Thu, 22 Sep 1994 12:16:27 -0700 Message-Id: <199409221916.MAA29075@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: model prep for Ewald sum calcs Does anyone have pointers to redistributable code for placing a molecule in a periodic box corresponding to crystal boundaries? I.e. 'drawing' the box so that the sides cut parts of the molecule(s) using the crystal parameters included in pdb files. Bill Ross From epw@ppco.com Thu Sep 22 16:05:21 1994 Received: from ppco.com for epw@ppco.com by www.ccl.net (8.6.9/930601.1506) id PAA18691; Thu, 22 Sep 1994 15:10:00 -0400 Received: from epwpc.ppco.com by ppco.com (/ ppco.1.0) id AA17749; Thu, 22 Sep 1994 14:09:12 -0500 Message-Id: <9409221909.AA17749@ppco.com> X-Sender: epw@charon.ppco.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 22 Sep 1994 14:12:07 +0100 To: ma_thompson@ccmail.pnl.gov, chemistry@ccl.net From: epw@ppco.com (Dr. Eric P. Wallis) Subject: Re: CCL:Periodic Systems & Commercial Codes X-Mailer: I use Polygraf 3.1 to do #1 and #2. I use Polygraf to generate input files to my Monte Carlo code (CChAPP written at Phillips). I can also visualize results from my MC runs using Polygraf. As to #3, I obtained a fortran program from MSI which translates their binary trajectory files to ASCII. Using that program, I can writes trajectory files in the format that Polygraf can read. One potential drawback with Polygraf, I think that the maximum number of atoms is 20,000. You might have to check this out. Unfortunely, MSI has discontinued Polygraf and I don't know how easily it will be to do the same with Cerius2 (I haven't tried yet). Hope this helps. Eric >I would like to hear about any commercial codes that can do the following: > >1). Solvate a molecule in an arbitrary box (for the purpose of setting up a > periodic system). > >2). Able to do #1 with any solvent molecule I specify. > >3). Has an openly defined molecular dynamics trajectory file format that > to which I can convert my MD trajectories, for the purpose of analysis > and visualization. Also, must be able animate MD trajectories and > do some "real" analysis, like rdf, average structural properties, etc. > >4). Is able to do the above on systems as large as 40K atoms. > > > >I know that Insight can do this. How about products like CAChe, HyperChem, >or any others out there. > >I have no great desire to run MD calculations with the computational >codes that come with these packages. Rather, I wish to interface capabilities >1-3 with our own MD codes. > > > > >---Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search >http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > *************************************************************** * Eric P. Wallis, Ph.D * * Computational Chemistry * * Phillips Petroleum Company Office (918)-661-7956 * * 331A PL PRC FAX: (918) 662-1097 * * Bartlesville, OK 74004 email: epw@ppco.com * *************************************************************** From epw@ppco.com Thu Sep 22 16:06:36 1994 Received: from ppco.com for epw@ppco.com by www.ccl.net (8.6.9/930601.1506) id PAA18876; Thu, 22 Sep 1994 15:21:17 -0400 Received: from epwpc.ppco.com by ppco.com (/ ppco.1.0) id AA25816; Thu, 22 Sep 1994 14:20:31 -0500 Message-Id: <9409221920.AA25816@ppco.com> X-Sender: epw@charon.ppco.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 22 Sep 1994 14:23:20 +0100 To: , chemistry@ccl.net From: epw@ppco.com (Dr. Eric P. Wallis) Subject: Re: CCL:md, equilibriation times and vibrations X-Mailer: I encountered this same problem working on a gas-phase molecule of 21 atoms. I was using velocity scaling, i.e., isokinetic techniques to mimic a canonical system. I noticed that my potential and internal kinetic energy were very much smaller that 3/2kT. Since I was in the gas phase, the translational and molecular rotational motions were virtual infinite sinks for energy since there was no need (or way) for the molecule to transfer kinetic energy back out of these modes in the gas phase. I fixed (worked around) the problem by initally subtracting our all of the translational and external rotational motion. Than, everytime I scaled the velocities to adjust the temperature, I would again subtract out the external motions. Since I was not interested in translational and external rotational motion of the molecule, this solved the problem. I don't know if this would work for your system or not. Hope this helps. Eric >I've encountered a problem with MD that experienced modellers may be able to >put my mind to rest about. Taking an isolated molecule (a mere 28 atoms) >which had been loosely geometry optimized, I turned it loose in a molecular >dynamics simulation using PM3 and monitored a few bond torsions and the >potential energy. (1 fs time step and .1ps bath relaxation). The potential >energy slowly drifted downward and after 20ps seemed to be assymptotically >approaching a binding energy of -2542 kcal/mole. During this time the >torsions which I was observing noticeably damped down substantially. > Afterwards I optimized the molecule, getting an energy of about -2546 >kcal/mole and started a new md run with the new structure with a heating >period of 1 ps to 300C. The potential energy leaped up about 25 kcal/mole >which seems about right (28 * 3/2 *(RT=.6kcal/mole)). The potential energy >is slowly settling back down and presumably will approach -2542 kcal/mole >again. Observing the damping out of the torsions and the small change in the >mean potential energy (4kcal/mole) between the minimized structure and the >equilibrium one, has lead to worry about where are the zero point vibrations. > When the simulations are started the atoms are given randomn directions >which basically excites all sorts of modes. As the molecule deexcites and >the bath carts off the excess energy all the bond vibrations (bends, >stretches and torsions) seem to be disappearing so that one is left with a >molecule travelling through space and spinning but that's all. I dusted off >my trusty old QM textbook and looked up 1-d harmonic oscillators. It pointed >out that zero point energy (that 1/2h(nu)) is a quantum mechanical effect >arising from the non-commutation of the positon and momentum operators (i.e. >the Heisenberg uncertainty principle raises its ugly head). Now in a >computer simulation of a molecule there is no such problem about commutation. > I can know both the position and momentum of the nuclei to arbitrary >accuracy. Does this mean that if I wait long enough the vibrations will all >freeze out completely and I'll be left with a spinning molecule careening >through space. One might also point out that it will be spinning and >careening far too fast since the bath will make sure the overall kinetic >energy, alot of which should be tied up in vibrations, is correct. Obviously >in a liquid, inter-molecular interactions will cause randomization of some >sort and pump energy back into vibrational modes. However, the whole thing >leaves me a little concerned about these kind of calculations. Can someone >out there reassure me? > >Ross Underhill >underhil@me2.rmc.ca > > >---Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search >http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > *************************************************************** * Eric P. Wallis, Ph.D * * Computational Chemistry * * Phillips Petroleum Company Office (918)-661-7956 * * 331A PL PRC FAX: (918) 662-1097 * * Bartlesville, OK 74004 email: epw@ppco.com * *************************************************************** From g8815205@mcmail.cis.mcmaster.ca Thu Sep 22 17:59:36 1994 Received: from mcmail.cis.mcmaster.ca for g8815205@mcmail.cis.mcmaster.ca by www.ccl.net (8.6.9/930601.1506) id RAA21507; Thu, 22 Sep 1994 17:47:29 -0400 Received: from PC-Hitchcock04-A.chemistry.McMaster.CA by mcmail.cis.mcmaster.ca with SMTP id AA08380 (931110.SGI/IDA-1.4.4); Thu, 22 Sep 94 17:46:33 -0400 To: chemistry@ccl.net From: "S.G. Urquhart" Cc: g8815205@mcmail.cis.mcmaster.ca, malott@mcmail.cis.mcmaster.ca Sender: g8815205@mcmail.cis.mcmaster.ca Subject: Wavefunction depositories by WWW? X-Originating-Host: [130.113.108.72] Reply-To: g8815205@mcmail.cis.mcmaster.ca Message-Id: <1994Sep22.175604-0400@[130.113.108.72]> Date: 22 Sep 1994 17:56:04 -0400 X-Mailer: BWMail for Windows Version 3.0c Hello chem.netters! A collegue has expressed interest in mounting a wavefunciton depository on the net, preferably by WWW. By this he means the *.wfn files from gaussian jobs. Has this been done elsewhere? Cheers, Stephen Urquhart g8815205@mcmail.cis.mcmaster.ca From awl1@midway.uchicago.edu Thu Sep 22 19:59:38 1994 Received: from midway.uchicago.edu for awl1@midway.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id TAA23525; Thu, 22 Sep 1994 19:15:24 -0400 Received: from quads.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Thu, 22 Sep 94 18:15:23 CDT Date: Thu, 22 Sep 94 18:15:06 CDT From: alpha beaver lo To: chemistry@ccl.net Subject: LIQUID/GAS CLUSTER SIMULATIONS Message-Id: I'm looking at simulating clusters (no periodic boundary conditions) as they change from liquid to gas, preferably at constant pressure. I'd appreciate any advice or tips to references thanks, alpha lo university of chicago awl1@midway.uchicago.edu