From szilagyi@almosvein.hu Mon Nov 11 12:18:26 1996 Received: from elod.vein.hu for szilagyi@almosvein.hu by www.ccl.net (8.8.2/950822.1) id LAA17571; Mon, 11 Nov 1996 11:57:18 -0500 (EST) Received: by elod.vein.hu (5.65/DEC-Ultrix/4.3) id AA01136; Mon, 11 Nov 1996 17:57:05 +0100 Received: from szilagyi.chemie.uni-marburg.de (pc15114.Chemie.Uni-Marburg.DE) by almos.venet (5.x/SMI-SVR4) id AA25300; Mon, 11 Nov 1996 18:54:24 +0100 Message-Id: <32875A6A.6639@almosvein.hu> Date: Mon, 11 Nov 1996 17:55:06 +0100 From: "Szilagyi, Robert K." Reply-To: szilagyi@almos.vein.hu Organization: =?iso-8859-1?Q?M=FCller?= Laboratory, Dept.Org.Chem., =?iso-8859-1?Q?Uni=2DVeszpr=E9m?=, HU X-Mailer: Mozilla 3.0 (Win95; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Unit of the force constant within the G94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Members, I am interested in the unit of force constants given in the output file of a Gaussian94 calculation. In the heading part of a frequency analyses the mDyne/A is given, but I receive nearly twice as it would be expected. I am tempting to say, that the unit is mDynd/Bohr instead of mDyn/A. Am I right? -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi Mueller Laboratory ph.d. student Dept. Organic Chemistry University of Veszprem szilagyi@almos.vein.hu Veszprem, H-8201 POB. 158; Egyetem u. 10. Phone: +36 88 422022 extn. 395 HUNGARY Mobile: +36 20 461413 (temp. susp.) Fax: +36 88 427492 http://mm1.vein.hu/ ====================================================================== ********** All opinions are my own, NOT my employer's ! ********** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From xiannong@pauling.chem.uga.edu Mon Nov 11 12:18:33 1996 Received: from charon.chem.uga.edu for xiannong@pauling.chem.uga.edu by www.ccl.net (8.8.2/950822.1) id LAA17281; Mon, 11 Nov 1996 11:13:14 -0500 (EST) Received: from pauling.chem.uga.edu ( [128.192.5.50]) by charon.chem.uga.edu (8.7.4/8.6.9) with SMTP id LAA13552 for ; Mon, 11 Nov 1996 11:16:38 -0500 Date: Mon, 11 Nov 1996 11:13:11 -0500 (EST) From: Xiannong Chen To: chemistry@www.ccl.net Subject: summary of using bar code system with chemical database Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here are all the e-mail I got about using bar code system with chemical database. I thank all the people who helped me. Xiannong =========================================================== Date: Thu, 07 Nov 1996 15:33:44 -0500 From: Heather Hunter To: xiannong@CCMSD.chem.uga.edu Subject: CCL Question Dr. Chen I saw your message on the CCL email this morning. Usually I do not respond to messages, being a commercial software company I think the bulletin board does a great job, and I do not wish to impose on line. Tripos has a desktop product called BioStar that might help you solve your problem of keeping track of your compounds. I can fax over some tech. notes for your if you are interested. Just drop me a email note. Thank you Heather ====================================================== Dear Xiannong, I asked some of my coworkers at MDL about their experiences with using barcodes in ISIS/Base and here is a summary of their responses. I hope this helps you get started. Bob Snyder Product Marketing Manager Database Business Unit MDL Information Systems ======================================================================== >From Bill Hackett (billh@mdli.com): I downloaded a barcode font for Mac from the Net for one of PaulM's customers. There is a font for PC; I've seen references to it. Let me know if you want the Mac font; I've got it on my machine. You can get the PC font in hits from Lycos with the search "macintosh barcode font". After that, its just a matter of changing the font for the numeric data. >From Frank Schaffer (franksch@ag.mdli.com): We have here in the AG developed an inventory system which tracks compounds and bottles containing these compounds as well as ordering for such compounds. It is based on ISISBASE and has indeed a barcoding interface. From this application you can print barcodes for bottles or for labels with user information (user privileges). It uses a barcode reader which is connected between the keyboard and the PC for regular one by one transactions of bottles. The system is also able to interact with a barcode scanner which collects multiple barcodes in it's memory and then sends them to the system (e.g. for updating bottles in a lab). The system also works with a balance to automatically check the contents of bottles. All the communication between this hardware pieces is done via the serial port using an external library (dll) which enables PL to write or read the com ports. >From Michael Edwards (michaele@mdli.com): Several company's have inserted bar code readers into their systems on consulting projects. We have used wedge-types and stand-alone systems. There are a lot of variables and trade off to consider before giving advice. >From Mitch Miller (mitch@mdli.com): Depending on what you want to do with barcodes, it can be pretty simple. If you just want to print barcode labels, or use barcodes to enter compound numbers, it's quite simple. To print barcodes, just set up one box to retrieve the company number in text format with a prefill trigger to take the text value, prepend/append an asterisk (required for 3 of 9, the most popular barcode font). The second box should have the font set to 3 of 9 or whatever. Then just print the form. Barcodes can be used to wand in a compound number just as if you were typing at the keyboard with no customization. ========================================================= -- Dear Xiannong Further to your email message of Thursday 7th November. We at Synopsys Scientific Systems Ltd develop chemical software which transforms Microsoft products into chemically intelligent databases and spreadsheets. The major area of interest to you may be Accord for Access, our chemical, relational, multi-user database. This software allows you to store and search chemical structures by exact, sub-structure and similarity all within the powerful environment of Microsoft Access. This Microsoft Access environment may be the ideal tool you are looking for as a barcoding system. We also develop Accord for Excel, the only true chemical spreadsheet on the market, allowing chemical data analysis all within the powerful environment of Microsoft Excel. If you would like to find out more about our suite of chemical software please contact me on any of the numbers below. I look forward to hearing from you. Yours sincerely Mark G. Vero Sales Executive E-Mail: mark@synopsys.co.uk Tel: +44 113 293 7339 ================================================================= Xiannong Chen wrote: > > Hi, Dear Netters: > > I work for a small pharmaceutical company. We want to use barcode to keep > track of our compounds. We use IsisBase to manage structural as well as > other information. Does anyone have experience with using barcode system > integrated with IsisBase or other database, spreadsheet software? > > Any suggestion about chemical inventary control with any software system > is appreciated. > > THank you very much. I am not on the list. Please sned your response to me > at xiannong@ccmsd.chem.uga.edu > > Xiannong > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: xiannong@pauling.chem.uga.edu > -- Original Sender From: Address: xiannong@CCMSD.chem.uga.edu > 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 I have put together a complete barcode system to track all of our commercial chemicals from cradle to grave. We use Daylight software and have barcode scanners in each lab. The barcode readers are hooked up to a pc that processes the data and then sends it over ethernet via an NFS mounted drive to our workstation. This makes it easily expandable as we can drop in new readers and pc anywhere we have ethernet ( which is everywhere in our company now). The data is processed into our ACD database which we buy from Daylight already in their format. I would think this system would be easily adaptable to your system using ISIS. Please call me for more info. -- Wayne Weber (weber@rl.cldx.com) Senior Dyemeister Johnson & Johnson Clinical Diagnostics Phone 716-453-5717 FAX 716-453-5689 From gmercier@mail.med.upenn.edu Mon Nov 11 17:12:46 1996 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.2/950822.1) id QAA19491; Mon, 11 Nov 1996 16:28:09 -0500 (EST) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.6.12/8.6.12) id QAA28854 for CHEMISTRY@www.ccl.net; Mon, 11 Nov 1996 16:28:06 -0500 From: "Gustavo A. Mercier Jr" Message-Id: <199611112128.QAA28854@mail.med.upenn.edu> Subject: P convergence in NPT MD runs - summary To: CHEMISTRY@www.ccl.net Date: Mon, 11 Nov 1996 16:28:05 -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, CClers! A few weeks ago I posted a message regarding convergence on the pressure in NPT simulations. The answers I received are below. In a nutshell, the pressure will not converge as tightly as the temperature. As explained by D. Case (and is detailed in the amber web paged mentioned below), the fluctuations will be large, ca. +/-100-150bars. Mean values close to +/-(1-10) bars can be obtained over long periods, ca. 100 ps. Bye! ***** Answers ******* ******************* If I understand correctly, what you are seeing is what is expected. At equilibrium, the "instantaneous" pressure will have what may seem like large fluctuations. These will never go away, and are related to the compressibility of the solvent. This is in the AMBER FAQ list: see http://www.amber.ucsf.edu/amber/amber.html go to "answers to commonly asked questions", and look for "constant pressure". This contains a disucssion of the behavior that one should expect, which sounds not too far from what you are seeing. ....hope this helps... ...dave case ********** Hi Gustavo, I have also had some problems like yours. I solved it by the following manner: 1.- I slightly increased the temperature for a few picoseconds, with the followinfg coupling constants: temperature 0.05 and pressure 0.5 ps. 2.- After this, I reduced the temperature to the original one, and I used a coupling constants of 0.1 and 0.5 for temperature and pressure respectivelly. If this does not work, I advise you to run a few picoseconds at constant volumen, followed of the steps 1 and 2 such as was described above. Good luck, Javier ******************************************************************************* Dr. Jose Javier Lopez Cascales | Office phone:Int-34-68-307100,ext:2190 * Departamento de Quimica-Fisica | Fax: Int-34-68-364148 * Fac. de Quimica, Uni. de Murcia, | e-mail: javier@fcu.um.es * Campus de Espinardo, 30071 Murcia, | www -> http://leonardo.fcu.um.es/~javier/* Spain | * ******************************************************************************* ************* Gustavo, As for the accuracy of the pressure calculation, it is always difficult to get very accurate value, because pressure is calculated by the virial theorem and it is calculated by subtracting a big value from a big value. The difference between the attractive and repulsive potential curve determines the value and makes the value not accurate. Moreover, you are using NPT ensemble and the particle system interacts with one dynamical system which represents external pressure. Therefore, simple oscillation may appear in the monitoring values. I think that if you add more non-linearity into the interaction between particle system and external pressure system, the equilibriation will be obtained more quickly. Best Regards, ----------------------------------------------------------------------- Masa Katagiri Queen's University of Belfast Atomistic Simulation Group http://titus.phy.qub.ac.uk School of Mathematics and Physics Tel:+44 1232 273528 Belfast BT7 1NN Fax:+44 1232 241958 Northern Ireland E-mail:m.katagiri@qub.ac.uk katagiri@nightmare.qub.ac.uk ----------------------------------------------------------------------- ******** Hi Gustavo, I have observed the same kind of behaviour. Pressure does converge more slowly and fluctuates more widely than Temperature. You could try tighter coupling; i.e. a smaller TAUP value. Note, though, tighter coupling for the Temperature (TAUTP) can lead to anomalous MD; I don't know whether the same thing can happen when the TAUP coupling constant is made very small. Cheers, Vidana C. Epa Biomolecular Research Institute, 343 Royal Parade, Parkville, Vic. 3052, AUSTRALIA. Tel: (61) - 3 - 9342 - 4300 Fax: (61) - 3 - 9342 - 4301 email: vepa@tigger.mel.dbe.csiro.au ******** Hi Gustav, as for the pressure fluctuations, if I were you I should not worry to much about that. The pressure is known to fluctuate enormously, and only the pressures averaged over sufficiently long periods (10-100ps) will have moderate fluctuations. So nothing is wrong in the system, except that if you have to tight coupling (and I think 0.1ps is already below the limit; I'd recommend 0.4ps for the pressure as the lower limit), you will not generate boltzmann-weigthed trajectories. The same holds for the T-coupling; do not couple to tightly. Hope this is of some help, Andrepeter Heiner. ================================================================= | Andreas P. Heiner | voice : +358-9-456 5105 | | VTT/Biotechnology and | fax : +358-9-455 2103 | | Food Research | e-mail: andrepeter.heiner@vtt.fi | | Biologinkuja 1, | | | PO Box 1500, Espoo | | | FIN-02044 VTT Finland | | ================================================================= ------------------------------------------------------------------------- Use a longer coupling constant for the pressure (0.5 or 1.0 ps) The fluctuations in the pressure are also dependent on the way the virial is computed: based on atoms, or based on molecules. The methods are in principle the same and do give the same averages. The atom based virial gives larger fluctuations. In our GROMACS code we have atom based virial and use at least 1.0 ps for the pressure coupling. David van der Spoel --------------------------------------------------------- EMAIL: spoel@chem.rug.nl WWW: http://rugmd0.chem.rug.nl/~spoel PHONE: 31-50-3634327 FAX: 31-50-3634800 MAIL: Nijenborgh 4, 9747 AG Groningen, The Netherlands. --------------------------------------------------------- --------------------------------------------------------- The pressure will never converge as you expect - please see amber41/Questions/pressure, or for the latest version, the version on our web site http://www.amber.ucsf.edu/amber/ Bill Ross --------------------------------------------------------- Gustavo, It is normal for the instananeous pressure to fluctuate wildly when one calculates the pressure from the "atomic" virial (there is a discussion in Allen and Tildesley about different ways to calculate pressure). If you average over 100 ps or so, then the AVERAGE pressure should be within a few atmospheres of your target. Before you invest a lot of CPU in this project, you might want to read a paper that Bernie Brooks, Rich Pastor and I published in JCP last year. JCP, 103, p 4613 (September 15, 1995 issue). There are some serious problems using the Berendsen method with an inhomogenous system, especially is SHAKE is used to maintain rigid water. Scott --------------------------------------------------------- Gustavo, < personal material deleted :-) > As regards your scientific question, I think that big fluctuations are a fact of life with constant pressure simulations - we use the same algorithm, and see the same behavior. Have you tried varying the coupling factor? I doubt that would accomplish a great deal, but I have never done (or seen) a systematic study. I cannot tell you off the top of my head if these big fluctuations are theoretically reasonable for a small ensemble of particles, or if the algorithm is to blame. Regards, Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@cyberjunction.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* ************* Hola Gus, Perdon por la demora por si alguien te contesto primero. La respuesta facil es: no hay problema con las fluctuaciones de la presion, y son solo producto de la compresibilidad del agua (TIP3). Aca va lo que dicen los expertos sobre el tema: I assume that the pressure should stablize at approximately 1. Except 1) the physics of pressure does not lend itself to instantaneous evaluation/correction and 2) the algorithm used by Amber (scaling the box & translating everything, and then applying SHAKE or letting bond, angle, etc. potentials rectify things) is not the best available. Having most values in the range -100..100 is the best I ever hope for w/ my 8-10000 atom dna/water systems. Note by Dave Case: -- pressure fluctuations are large because the pressure-volume isotherm of a liquid is extremely steep: it takes a large pressure change to yield a small volume change, and conversely: a volume that is instantaneously slightly out of equilibrium yields a large pressure. The fluctuations in pressure are then related to this: in a thermodynamic sense (e.g. Landau & Lifshitz, "Statistical Physics" sec. 114): mean value of (delta p)**2 = -kT(dp/dV) where the derivative is evaluated at constant S (!). Rearranging the above equation, approximating (dp/dV) at constant S by 1/(dV/dp) at constant T, yields (delta p)**2 = kT/(V*beta) or delta p ~= sqrt(1/beta) where beta is isothermal compressibility and I have set kT/V to 1 bar in the final equation. If we use the macroscopic value for beta for water (roughly 4 x 10**-5 bar**-1) we obtain an rms pressure fluctation microscopic ideas: pressure fluctuations in very small volumes would probably be larger than this. Having said this, it must be noted that the procedure used in Amber (based on ideas of Berendsen) does not generate a simple thermodynamic ensemble, and (in addition) should not be expected to yield fluctuations that match the thermodynamic formula cited above. It will be interesting to see if anyone reports a systematic study of these numbers as a function of the type of simulation being done (especially on the volume of the simulated system.) --- ************ ... I have done a large amount of dynamics with periodic boundaries [in charmm]. I believe you can reasonably use about 1 to 100 atmospheres without any real perturbation. My experimental work in my job indicates little pressure effects on most systems of common interest. Besides, the RMS deviation of the pressure in the system is related to the compressability of the system and thus there is a finite and large variation in the internal pressure. The internal pressure of the system will be a strong function of the temperature at which the dynamics are conducted. One approach is to use a boundary which gives a water density very close to standard tables for the given temperature. I have noticed that sometimes this can be incorrect as the second phase (or solute) can have too low of a density. Just recently I have taken a new approach (at least it is new for me). Since standard CHARMm output does not give any idea of the internal pressure or pressure fluctuations for constant volume dynamics, I have started looking at the potential energy of the system as the boundary is decreased. That is, about 5 ps of dynamics are conducted and the average potential energy at the end is recorded. The periodic boundary is then reduced by 0.1 Angstroms and the dynamics restarted for another 5 ps. The procedure is repeated for for several steps of boundary reduction. One will observe a sharp increase in potential energy as the system reaches a pressure of about 1 - 10 atmospheres. This procedure assumes that the initial periodic boundary was too large for the system being studied. In addition, I should mention that the size of my systems range from about 40 Ang on a cubic edge to 60 Ang. on a cubic edge. You may have to take smaller step sizes than I do. --- User dialogue with Dave Case: > in Sander output files (standard name: mdout and mden) values > of the pressure are reported. I'm wandering in which unit > this values are given. I would gess "mbar", but maybe > somebody knows it exactly. A futher problem with the pressure is > that I have got negative values. What does negative values mean? > Is the pressure given as relative pressure? Pressures are reported in bars; negative pressures indicate that the system would like to contract its volume, i.e. that an outward force on the walls of the container would be required to keep the system at its current volume; positive pressure is the opposite: the system would like to increase its volume, and an inward-directed external force would be required to keep the system at its current volume. > As the reported pressure is the absolute pressure I would suggest to > interpret the values in the following way: > > If the instantaneous pressure is greater than PRES0 the system > wants to increase is volume (overpressure); if the instantaneous pressure > is lower than PRES0 but greater than zero the system wants to contract its > volume (subpressure); an instantaneous pressure below zero > is an artifact due to the way the virial term is calculated. I must say that I don't agree with your interpretation.... The pressure is computed from the virial in the standard way. The only influence of PRES0 is on how the volume of the system will respond: if the instantaneous pressure is greater than PRES0, the MD algorithm in Amber will slowly increase the volume of the system; vice-versa if the instantaneous pressure is below PRES0. The *interpretation* of the computed pressure is independent of the value of PRES0. There is nothing "wrong" with negative pressures, and they need not arise from errors or truncations in the virial calculation. The equation of state of a rare gas fluid (for example) has substantial regions of density and temperature where the equilibrium pressure is negative [see, for example, chapter 14 of McQuarrie's "Statistical Mechanics", or other textbooks.] One of the tests I made (many years ago) to verify the correctness of the way Amber calculates pressure terms was to reproduce these equations of state for a Lennard-Jones 6-12 fluid. [One can hope that bugs have not crept in since then!] -- Adrian E. Roitberg ======================================================================== National Institute for | Phone: (301) 975-4469. Fax (301) 330-3447 Standards and Technology | E-mail : adrian@nist.gov Bioprocess Engineering Group | Building 222, A-353 | URL : http://www.chem.nwu.edu/~adrian Gaithersburg, MD 20899 | ======================================================================== -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843