From Gerald.Loeffler@univie.ac.at Tue Jul 8 06:50:37 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id GAA14110; Tue, 8 Jul 1997 06:25:15 -0400 (EDT) Received: from gerilap.imp.univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id MAA43956 for ; Tue, 8 Jul 1997 12:24:43 +0200 Message-ID: <33C21478.4B70@univie.ac.at> Date: Tue, 08 Jul 1997 12:20:40 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: SUMMARY: Removing Translation and Rotation after MD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Quite some time ago (sorry) I asked how exactly to remove translation and rotation of a molecule after an MD simulation, because I felt that a simple superimposition of all the structures to the start structure such that the rmsd deviations of respective atoms is minimal might not allways be appropriate. A special "Thank You" to Paul Soper Frederic A. Van-Catledge Konrad Hinsen Michael K. Gilson Andrew Dalke for taking the time to answer. The bottom line for me is as follows: Removing translation and rotation works _exactly_ only for the rigid rotator. Since I'm analyzing proteins which are quite far away from being rigid, there is not _one_ way of removing translation and rotation. So I might as well just superimpose the structures as I've allways done it (using profit). Furthermore, this method is guaranteed to work, whereas methods based on the inertia tensor might run into ambiguity problems or might align the proteins in surprising ways (wrong handedness, ...). Thanks to all who responded!! gerald ======================================================================== My original question: I need to remove the translational and rotational motion of a protein after a Molecular Dynamics simulation. I know, this is a seemingly trivial problem. A) Up to now I didn't care much about the details and just fitted all protein structures along the MD trajectory to the start structure such that the C-alpha atoms are optimally (i.e., minimal root-mean-square deviation) superimposed (e.g. using the excellent profit program). B) However, it may be that for my current problem the other alternative that came to my mind would be better suited, namely 1) removing translation by superimposing the centers of gravity of all structures and subsequently 2) removing rotation by superimposing the "principal axes of inertia" of all structures. Firstly, I'm not sure if the terminology of B)2) is correct. Secondly, I'm missing the formulas to do B)1) and B)2). Thridly, I'd like to know if there are cases where either method A) or method B) are definitely prefered. Fourthly, it may be that there are other methods of removing translation and rotation?! Fifthly, which free program implements method B) or other intersting methods? ======================================================================== Paul Soper: Many molecular modeling programs include the ability to do both the translation and rotation you describe. The math is simple and should be in any introductory quantum text under a discussion of 'the rigid rotor.' You're welcome to the source code of program I wrote (in 'C') which does what you want. The input and output formats for the molecular structure are probably not those you'd prefer, but it would certainly give you a starting point. Please let me know if you'd like a copy. ======================================================================== Frederic A. Van-Catledge: There are any number of code (fragments) floating around that will do both steps in your option B. The trick is to insure that you do not generate the optical antipode in the process. This can be done by, after diagonalization of the moment of inertia tensor, applying the transformation to the unit vectors of the starting coordinate system. One then applies a "handedness" check to the new unit vectors. If the "handedness" has changed, one does a sign-flip on one set (x, y, or z) of the new coordinates. selecting the correct one can get a little tricky, I suspect, if you are trying to preserve continuity in an MD trajectory. ======================================================================== Konrad Hinsen: (in German, as you will notice...) > A) Up to now I didn't care much about the details and just fitted all > protein structures along the MD trajectory to the start structure such > that the C-alpha atoms are optimally (i.e., minimal root-mean-square > deviation) superimposed (e.g. using the excellent profit program). Und dagegen spricht auch nichts. > B) However, it may be that for my current problem the other alternative > that came to my mind would be better suited, namely > 1) removing translation by superimposing the centers of gravity > of all structures > and subsequently > 2) removing rotation by superimposing the "principal axes of > inertia" of all structures. Das fuehrt zum selben Ergebnis mit mehr Aufwand. Noch eine aequivalente Methode, die auch sehr effizient ist, ist die direkte Umsetzung der Definition: man berechnet den Gesamtimpuls P, den Gesamtdrehimpuls T, und den Traegheitstensor I, Schritt fuer Schritt entlang der Trajektorie. Daraus berechnet man die Schwerpunktsgeschwindigkeit P/M (M = Gesamtmasse) und die Rotationsgeschwindigkeit (I^(-1) * T), und zieht beide von den atomaren Geschwindigkeiten ab. Das ist die einfachste und schnellste Methode, wenn man die Geschwindigkeiten hat oder berechnen kann. Wenn man nur einzelne Konfigurationen hat, bleibt nur der Fit. > Fifthly, which free program implements method B) or other intersting > methods? Eigentlich sollte jedes Programm, dass MD-Trajektorien erzeugen kann, auch eine Option zur Eliminierung der Translation und Rotation haben! ======================================================================== Michael K. Gilson: I don't think your question is "trivial". I think there are multiple answers that are potentially "correct", because the question is ambiguous. Before embarking upon a discussion of these issues, I'll say that the bottom line of my response is that the proper way to handle this will depend upon precisely what it is you want to accomplish. That is, why do you need to remove these motions? Now for the discussion: 1) To begin, the words "translation" and "rotation" are ambiguous. Recall that the molecular partition function involves integrals over both momentum and position. Therefore, in the fullest sense of the words, "translation" and "rotation" refer not to 6 but to 12 degrees of freedom: 6 spatial coordinates and 6 momenta. Therefore, if you want to "remove the translational and rotational motion of a molecule", it is not clear whether you are worrying about a) the translation and rotation of a molecule *in space*; b) the translational and rotational *momentum* of a molecule. 2) The traditional separation of translational and rotational degrees of freedom from the internal degrees of freedom of a molecule is much more natural for an essentially rigid molecule than for a flexible one. Thus, stat thermo courses and books use this separation in the context of the rotor-harmonic oscillator approximation for a diatomic molecule. For such a molecule, the vibrations have very little effect upon the rotational moments of inertia and therefore are separable from external rotations to a good approximation. I would not trust that this separation would hold to a good approximation for a flexible molecule. This said, people *have* made this separation when using normal mode analysis of proteins. This seems reasonable so long as one is willing to live with the rather drastic harmonic approximations required for normal mode analysis. Given these approximations, the rigid rotor-harmonic oscillator approximation seems okay. 3) As noted above, you might be interested in either the momenta or the spatial coordinates. If you are interested in spatial coordinates, then it turns out that rotation and translation are still ambiguous. The reason is that one can separate internal from external (translation/rotation) coordinates in any number of ways (Biophys J. 35:7819,1996). For example, one can define the "position" of the molecule as the position of its center of coordinates; all other atomic positions are then defined relative to this center. But one can also define the "position" of the molecule as the position of atom number 1, for example. It is just as legitimate to define the positions of all other atoms relative to atom 1 as to the center of coordinates. The orientation of the molecule in space is similarly ambiguous. In summary, the position and orientation in space are ambiguous for flexible molecules. Well, this has probably made you more rather than less confused! So I return to the bottom line: the real answer to your question depends upon what precisely you wish to accomplish. ======================================================================== Andrew Dalke: I don't think the aligning of the principal axes of inertia would work too well. Consider uranium hexaflouride. Its elliposoid of inertia is a sphere but it is not rotationally symmtetric. Your alignment would stop saying there was a degeneracy whereas an RMSD alignment would not have a problem. > it may be that there are other methods of removing translation > and rotation?! The one I used is Kabsch, Acta Cryst. (1978) A34, 827-828, which does one way of doing RMSD alignment. ======================================================================== -- Gerald Loeffler PostDoc in Theoretical Biophysics EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From yubofan@guomai.sh.cn Tue Jul 8 12:50:41 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id MAA16003; Tue, 8 Jul 1997 12:00:45 -0400 (EDT) Received: from aopen-k6-166 ([210.0.0.27]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id AAA23661 for ; Wed, 9 Jul 1997 00:56:54 +0800 Message-Id: <199707081656.AAA23661@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Which method is better for a rather big molecule. Date: Tue, 8 Jul 1997 23:59:08 -0000 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=HZ-GB-2312 Content-Transfer-Encoding: 8bit Hi, Thanks for the advice. Here's the summary. Hi, All, I want to optimize the conformations of some big molecules, for example, N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable for this kind big system. Also, some semi-empirical methods are not accurate enough for such calculations. Which method can do this kind work? Thank you very much! Y. FAN -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: yubofan@guomai.sh.cn -- Original Sender From: Address: yubofan@guomai.sh.cn 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 =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 =================================================== Hello, Your molecule is not as big as you think. Have you tried the RIS method to find the minimum potential energy conformation ? My friends once studied the polybenzozaxine dimer using this method, and it worked very well. But you have to write the code or find a package containing RIS module. Good luck. On Mon, 16 Jun 1997, [CN-GB] ~{76S}2(~} wrote: > Hi, All, > > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not > accurate enough for such calculations. > > Which method can do this kind work? > > > Thank you very much! > > Y. FAN > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: yubofan@guomai.sh.cn > -- Original Sender From: Address: yubofan@guomai.sh.cn > 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 > A classic way of handling a molecule of this size is to break it down to logical pieces. Perhaps do at least two optimizations 1) N-ethyl-N-methylanaline, 2) N-dimethyl-N-alkylamine. Personally, I don't know of any other way. -- Luke Anthony Burke tel:609-225-6158 (-6142) Professor and Chair, fax:609-225-6506 Department of Chemistry e-mail: Rutgers University burke@camden.rutgers.edu Camden, NJ 08102, USA http://camchem.rutgers.edu/~burke > Hi, All, > > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not > accurate enough for such calculations. > > Which method can do this kind work? > > > Thank you very much! > > Y. FAN I think the best way is to do a DFT calculation, starting with B3LYP/4-31G DFT is a good method for large molecules. bye, *-----*-----*-----*-----*-----*-----*-----* / / / Anselmo Elcana de Oliveira / * Cidade Universitaria Zeferino Vaz * / IQ - UNICAMP CEP 13083-970 \ / Campinas, SP - Brasil \ * elcana@iqm.unicamp.br * / http://chope.iqm.unicamp.br \ / \ * To err is human, * / To really foul up requires the root password \ / \ *-----*-----*-----*-----*-----*-----*-----*-----*-----*-----* You may use RHF with small basis sets. However, it still depends how many memory your computer has. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Mon, 16 Jun 1997, [CN-GB] ~{76S}2(~} wrote: > Hi, All, > > I want to optimize the conformations of some big molecules, for example, > N-methyl-N-octadecylanaline. I think RHF or DFT methods are not suitable > for this kind big system. Also, some semi-empirical methods are not > accurate enough for such calculations. > > Which method can do this kind work? > > > Thank you very much! > > Y. FAN > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: yubofan@guomai.sh.cn > -- Original Sender From: Address: yubofan@guomai.sh.cn > 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 > > Optimize? You did not indicate what you wish to optimize but I shall assume that you are looking for the global minimum, i.e. the conformation with the minimum energy. This is a non-trivial task and you want to use classical methods to search conformational space for candidates. I use molecular dynamics at 1000 K or 2000 K. I have also used Crippen's distance geometry algorithm. Jeff Blaney has written a nice implementation of distance geometry which is available through QCPE. Once you have sampled conformational space, you need to minimize each structure using molecular mechanics and then sort the structures as to energy. If you want a good ab initio energy, you then want to apply quantum-mechanical methods to the best structures identified by the classical approach. You won't be able to do the entire problem quantum mechanically. Millions of structures are involved. From yubofan@guomai.sh.cn Tue Jul 8 12:50:50 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id MAA16002; Tue, 8 Jul 1997 12:00:44 -0400 (EDT) Received: from aopen-k6-166 ([210.0.0.27]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id AAA23657 for ; Wed, 9 Jul 1997 00:56:38 +0800 Message-Id: <199707081656.AAA23657@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Want a program to control CPU time. Date: Tue, 8 Jul 1997 23:39:55 -0000 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=HZ-GB-2312 Content-Transfer-Encoding: 7bit Hi, Thank everyone who gave me some advice and read the message I posted several weeks ago. That is the summary below. Hi, everyone, I use G94W to calculate some molecular systems on my PC. My OS is Windows 95. When the calculations are running, all CPU time is used by this software and I cannot run other software easily. Is there a program which can allocate a part of time to a certain program, for instance, the program can allocate 90% CPU time to G94W and other software can use another 10% resourses? If there is one, please tell me. I really need it. Thank you very much Y. FAN =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 =================================================== On Thu, 3 Jul 1997, Yubo Fan wrote: > Hi, everyone, > > I use G94W to calculate some molecular systems on my PC. My OS is Windows > 95. When the calculations are running, all CPU time is used by this > software and I cannot run other software easily. Is there a program which > can allocate a part of time to a certain program, for instance, the program > can allocate 90% CPU time to G94W and other software can use another 10% > resourses? > > If there is one, please tell me. I really need it. There is one -- it's called Linux. Win95 cannot do true multitasking. You also might consider upgrading to NT... but Linux is a better choice ;) Eugene > Thank you very much > > Y. FAN > > =================================================== > FAN, Yubo > Department of Chemistry > Fudan University > Shanghai, 200433 > P. R. China Voice(86-21)65492222-4294 > =================================================== > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > Maybe you should just try to use an real operating system to do this kind of work on ? There are many good OSs for PC's out. Usin W95 is your own fault. Sorry that's it, Jochen ----------------------------------------------------------------------- Jochen Kuepper Heinrich-Heine-Universitaet Duesseldorf jochen@uni-duesseldorf.de Institut fuer Physikalische Chemie I Universitaetsstrasse 1, Geb 26.43.02.19 phone ++49-211-8113681 40225 Duesseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- > I use G94W to calculate some molecular systems on my PC. My OS is Windows > 95. When the calculations are running, all CPU time is used by this > software and I cannot run other software easily. Is there a program which > can allocate a part of time to a certain program, for instance, the program > can allocate 90% CPU time to G94W and other software can use another 10% > resourses? Not for Windows 95. Under Unix systems, you can use the commands "nice" and "renice". There may be something equivalent under Windows NT, but Windows 95 doesn't have a proper process scheduler. -- ---------------------------------------------------------------------------- --- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ---------------------------------------------------------------------------- --- Dear YAN, I think you have two possibilities first upgrade your Gaussian Version to a 32-bit Version, second switch e.g. to Spartan for Windows 95. This program cooperates very smothley with the environment, and lets you work very well with other programs. For my knowledge there is no mechanism in Windows 95 to specify the amount of CPU usage for a specific program. But windows 95 knows priorities for 32-bit programs and uses time slices for each 32-bit program. Greetings, Jan Schuur -------------------------------------------------------------------------- Jan H. Schuur Ph.D. Student Computer-Chemie-Centrum Institut f. Org. Chemie Universitaet Erlangen-Nuernberg Naegelsbachstr. 25 D-91052 Erlangen, Germany Tel. ++49 (0)9181 658577 ------------------------------------------------------------------------- Hello. I've had good results running G94W under Windows NT (4.0). While G94W is running, performance on other applications is degraded but usually acceptable. My machine has 64 Mb of RAM. A couple of years ago I tried G92w under Windows 3.1 and gave up because of problems like you described. Good luck! Karl I. At 10:34 AM 7/3/97 +0800, you wrote: > >Hi, everyone, > >I use G94W to calculate some molecular systems on my PC. My OS is Windows >95. When the calculations are running, all CPU time is used by this >software and I cannot run other software easily. Is there a program which >can allocate a part of time to a certain program, for instance, the program >can allocate 90% CPU time to G94W and other software can use another 10% >resourses? > >If there is one, please tell me. I really need it. > >Thank you very much > >Y. FAN > >=================================================== >FAN, Yubo >Department of Chemistry >Fudan University >Shanghai, 200433 >P. R. China Voice(86-21)65492222-4294 >=================================================== > > >--- >Administrivia: This message is automatically appended by the mail exploder: >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 >--- > > > ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-975-3670 e-mail: karl.irikura@nist.gov ---------------------------------------------- From yubofan@guomai.sh.cn Tue Jul 8 15:56:16 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id PAA17128; Tue, 8 Jul 1997 15:21:11 -0400 (EDT) Received: from aopen-k6-166 ([210.0.0.3]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id EAA02270 for ; Wed, 9 Jul 1997 04:17:13 +0800 Message-Id: <199707082017.EAA02270@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Why does G94W's SCF option make errors? Date: Wed, 9 Jul 1997 03:18:47 -0000 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=HZ-GB-2312 Content-Transfer-Encoding: 8bit Hi, I got many help from the CCL. Every advice is important for me, and some of them cannot be read from books or Jounals. Thank you very much. Here's the summary. Hi, ccl'ers, I calculated a molecule with 3 Phenyls. I use BLYP/3-21G**. This time, I try "restart", a SCF option that I didn't use before. I kill the job after L502.exe had been running 4 cycles, then I put "restart" after "SCF=". I ran the calculation again. L502.exe did 2 cycles and the result was gotten. Again I did the job from the very original start. After 6 cycles had been done, another result was gotten. I list them below: :With SCF=(save, restart) Convergence on energy, delta-E=1.12D-05 SCF Done: E(RB-LYP) = -692.644057005 A.U. after 2 cycles Convg = 0.2054D-03 -V/T = 2.0090 S**2 = 0.0000 KE= 6.864357999909D+02 PE=-3.864671343753D+03 EE= 1.355127785196D+03 :With SCF=save SCF Done: E(RB-LYP) = -692.644408415 A.U. after 6 cycles Convg = 0.4070D-05 -V/T = 2.0094 S**2 = 0.0000 KE= 6.861718246427D+02 PE=-3.864945652472D+03 EE= 1.355665717853D+03 Why do they have error I think it considerable great? Thanks a lot Y. FAN =================================================== FAN, Yubo Department of Chemistry Fudan University Shanghai, 200433 P. R. China Voice(86-21)65492222-4294 =================================================== --- Administrivia: This message is automatically appended by the mail exploder: 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 --- Re your message about BLYP/3-21G**, in case you didn't get an answer yet : Here, you did a Single-Point calculation, I presume. The Cut-Offs for these calcs are quite loose, thus the _small_ difference in energy (.027 mH, .04 kcal/mol). Start it from yet a different position, you'll get a third, also diff. number. This problem is I think more significant with DFT than with HF. If you want 7-8 significant digits, use the option scf(nosp) or scf(tight) when you do single points. Nest of luck Jeremy 1. This is not a SCF calculation, it is at BLYP (DFT) level. 2. Are you sure that molecular geometryies are identical? ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Tue, 24 Jun 1997, ~{76S}~}#~{( ~}wrote: > > Hi, ccl'ers, > > > I calculated a molecule with 3 Phenyls. I use BLYP/3-21G**. This time, I > try "restart", a SCF option that I didn't use before. I kill the job after > L502.exe had been running 4 cycles, then I put "restart" after "SCF=". I > ran the calculation again. L502.exe did 2 cycles and the result was gotten. > Again I did the job from the very original start. After 6 cycles had been > done, another result was gotten. I list them below: > > :With SCF=(save, restart) > Convergence on energy, delta-E=1.12D-05 > SCF Done: E(RB-LYP) = -692.644057005 A.U. after 2 cycles > Convg = 0.2054D-03 -V/T = 2.0090 > S**2 = 0.0000 > KE= 6.864357999909D+02 PE=-3.864671343753D+03 EE= 1.355127785196D+03 > > :With SCF=save > SCF Done: E(RB-LYP) = -692.644408415 A.U. after 6 cycles > Convg = 0.4070D-05 -V/T = 2.0094 > S**2 = 0.0000 > KE= 6.861718246427D+02 PE=-3.864945652472D+03 EE= 1.355665717853D+03 > > > Why do they have error I think it considerable great? > > > Thanks a lot > > Y. FAN > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > > Dr. Fan, If you look at the convergence of the two cases you see that they agree to the convergence criteria of the restarted job. Based on the information you supplied it is not clear why G94W would have stopped at this point as the RMS change in the density, the value listed as Convg, is larger than the default criteria. If you ran these with #P you can look at the status at each iteration and perhaps we can get a clue. Also include the information about what revision of G94W you are running. > Hi, ccl'ers, > > > I calculated a molecule with 3 Phenyls. I use BLYP/3-21G**. This time, I > try "restart", a SCF option that I didn't use before. I kill the job after > L502.exe had been running 4 cycles, then I put "restart" after "SCF=". I > ran the calculation again. L502.exe did 2 cycles and the result was gotten. > Again I did the job from the very original start. After 6 cycles had been > done, another result was gotten. I list them below: > > :With SCF=(save, restart) > Convergence on energy, delta-E=1.12D-05 > SCF Done: E(RB-LYP) = -692.644057005 A.U. after 2 cycles > Convg = 0.2054D-03 -V/T = 2.0090 > S**2 = 0.0000 > KE= 6.864357999909D+02 PE=-3.864671343753D+03 EE= 1.355127785196D+03 > > :With SCF=save > SCF Done: E(RB-LYP) = -692.644408415 A.U. after 6 cycles > Convg = 0.4070D-05 -V/T = 2.0094 > S**2 = 0.0000 > KE= 6.861718246427D+02 PE=-3.864945652472D+03 EE= 1.355665717853D+03 > > > Why do they have error I think it considerable great? > > > Thanks a lot > > Y. FAN > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > Douglas J. Fox Director of Technical Support help@gaussian.com Dr. Fan, There was a condition with Rev. B.3 where G94W could incorrectly decide that the SCF had converged because the energy increased. This has been corrected and may be the cause of your problem. While the SCF=Restart option can save you time you must continue to check the result to make sure it is reasonable, as you must with any computational procedure. > Dr. Fox, > > > The Calculation Package I use is Gaussian 94 Revision-B.3. > > I will do a big job later, so I must do a test for occasional poweroff or > system crack. I kill the job after 4 cycles have done, then I retake the > job with option restart. > > Thanks for your help. > > Y. FAN > Douglas J. Fox Director of Technical Support help@gaussian.com From ccl@www.ccl.net Tue Jul 8 21:50:46 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id VAA18801; Tue, 8 Jul 1997 21:42:07 -0400 (EDT) Received: from auric.chem.csiro.au for Dave.Winkler@molsci.csiro.au by bedrock.ccl.net (8.8.6/950822.1) id VAA06981; Tue, 8 Jul 1997 21:42:00 -0400 (EDT) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA20702 (5.67b/IDA-1.5 for chemistry@ccl.net); Wed, 9 Jul 1997 11:38:50 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 Jul 1997 11:40:48 +1000 To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: ORAC reaction database Cc: george.holan@molsci.csiro.au Hi, Netters, Does anyone know the fate of the ORAC chemical reaction database? It is quite old now and probably not sold or supported. We have a copy and would like to move the reactions into another program but need to know about the database structure, or file export capabilities of the prgram. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Division of Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC, http://www.csiro.au Clayton 3169, Australia http://www.molsci.csiro.au