From darren@tau.ucg.ie Thu Jul 10 07:51:07 1997 Received: from tau.ucg.ie for darren@tau.ucg.ie by www.ccl.net (8.8.3/950822.1) id HAA28267; Thu, 10 Jul 1997 07:23:51 -0400 (EDT) Received: by tau.ucg.ie (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id NAA24931; Thu, 10 Jul 1997 13:15:14 GMT From: "Darren D'Arcy" Message-Id: <9707101315.ZM24929@tau.ucg.ie> Date: Thu, 10 Jul 1997 13:15:08 +0000 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Ring Interactions/Proteins Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, I am doing a research Ph.D in protein crystallography. The proteins that i work with, uses FMN as a cofactor ( a 3 membered ring consisting of a di methyl 6 membered ring a pyrazine ring and a pyrmidine subnucleus ( collectively called isoalloxazine)). It is sandwiched between 2 hydrophobic residues, Tyrosine (a phenyl with an OH) above the ring and Tryptophan below the ring system. I would be interested in investigating semi emperically the interaction of the tyrosine and the isoalloxazine. The rest of the protein could be ignored. As my main concern is crystallography it should not be too time consuming. Does anyone have any ideas? All replys would be very much appreciated. E-mail darren@tau.ucg.ie -- Darren. From yubofan@guomai.sh.cn Thu Jul 10 09:51:07 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id JAA29024; Thu, 10 Jul 1997 09:40:07 -0400 (EDT) Received: from aopen-k6-166 (dhcp01.belrose.visionet.com.au [210.0.0.19]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id WAA20460 for ; Thu, 10 Jul 1997 22:36:13 +0800 Message-Id: <199707101436.WAA20460@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Which method is better for a rather big molecule. Date: Thu, 10 Jul 1997 21:38:18 -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 Thu Jul 10 09:51:16 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id JAA29020; Thu, 10 Jul 1997 09:39:59 -0400 (EDT) Received: from aopen-k6-166 (dhcp01.belrose.visionet.com.au [210.0.0.19]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id WAA20452 for ; Thu, 10 Jul 1997 22:36:02 +0800 Message-Id: <199707101436.WAA20452@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Want a program to control CPU time. Date: Thu, 10 Jul 1997 21:37:10 -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 Thu Jul 10 09:51:23 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id JAA29028; Thu, 10 Jul 1997 09:40:18 -0400 (EDT) Received: from aopen-k6-166 (dhcp01.belrose.visionet.com.au [210.0.0.19]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id WAA20472 for ; Thu, 10 Jul 1997 22:36:22 +0800 Message-Id: <199707101436.WAA20472@gm-email.guomai.sh.cn> From: "Yubo Fan" To: Subject: Summary: Why does G94W's SCF option make errors? Date: Thu, 10 Jul 1997 21:40:08 -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, 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 andy@neptune.chem.uga.edu Thu Jul 10 12:15:18 1997 Received: from neptune.chem.uga.edu for andy@neptune.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id LAA29598; Thu, 10 Jul 1997 11:12:24 -0400 (EDT) Received: (from andy@localhost) by neptune.chem.uga.edu (8.7.4/8.7.3) id LAA16346 for CHEMISTRY@www.ccl.net; Thu, 10 Jul 1997 11:13:04 -0400 Date: Thu, 10 Jul 1997 11:12:57 -0400 (EDT) From: Andy Dustman Sender: andy@neptune.chem.uga.edu To: CHEMISTRY@www.ccl.net Subject: Subscribe to G, the GAUSSIAN mailing list Message-ID: -----BEGIN PGP SIGNED MESSAGE----- G is a mailing list devoted exclusively to the GAUSSIAN series of programs. With over 130 subscribers, someone is bound to have the answer to your question. (General computational chemistry questions should continue to be directed to CCL.) To subscribe to G, send mail with the subject "subscribe" to: g-request@ccmsd.chem.uga.edu Andy Dustman / Computational Center for Molecular Structure and Design / UGA To get my PGP public key, send me mail with subject "send file key". For the ultimate anti-spam procmail recipe, send me mail with subject "spam" "Encryption is too important to leave to the government." -- Bruce Schneier http://www.ilinks.net/~dustman mailto:andy@CCMSD.chem.uga.edu <}+++< -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv iQEPAwUBM8T7/ROPBZTHLz8dAQG+BQfLB+CgFwknV03fGvtDrjfkSqV6yoiZ1hdK aGLeH7aa30L9UDG++u3+h+PSxtpUYOwwUz2OpqX+dcXy/eellGuzoyXjlpYqBT1g HXNxh6Ab7VdH9TGpiheFCd6irDtAiBkd39iy0eJJ82vI4YcwNqgJst1ihaib0nqK YkGhlkSNfKukd0B9FdQ8XhecnfIjS2BNFkM75BgRSWWo4dRTUmnL7HHgayBNefRO FzZk7AQTsv3kjM3p+dFZDAKhwGnenW8JpRux9TPd1atxb5K07uJSpK9V/8lOe+Cl 70Bp+QRHfOOxNXURotjdTGEvCUoFT3RepwUAjw/hUyBQ5g== =iRLN -----END PGP SIGNATURE----- From daizadeh@kappa.ucdavis.edu Thu Jul 10 14:06:11 1997 Received: from kappa.ucdavis.edu for daizadeh@kappa.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id NAA00470; Thu, 10 Jul 1997 13:14:17 -0400 (EDT) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA14978; Thu, 10 Jul 1997 10:12:28 -0700 Date: Thu, 10 Jul 1997 10:12:28 -0700 From: daizadeh@kappa.ucdavis.edu (Iraj Daizadeh) Message-Id: <199707101712.KAA14978@kappa.ucdavis.edu> To: daizadeh@kappa.ucdavis.edu, CHEMISTRY@www.ccl.net, chemistry-request@www.ccl.net Hello. Below is a summary of the responses I have received concerning visualization of 3-D data, in particular, visualization of a 3-d flow field. I have also included possible solutions to a recent problem sent to the CCL which corresponds to a related aspect of data analysis; viz., visualization of some sort of iso-surface (generalized contouring). I have attempted to make all listings below as anonymous as possible (plagarism). For the most part, all programs shown below were compiled (or precompiled binaries used) on a SGI (SiliconGraphics,Inc.) R10000 running IRIX 6.2 (except for the Fortner products). I should note that there were many others I have tested as well; a list of those follow: Plotmtv - Great, almost as easy as xmgr!!!!!! YetAnoextHuckMolorbprog - Nice for display of band structures, etc. graph3d - robot - scian - tecate - tipsy - uncert - The last six are vacuous since either I do not remember the programs efficacy or there were compilation problems. Any questions, comments or concerns, please do not hesitate to send me an email. Iraj. P.S. I should note that Vu is a beautiful program that has aided us in our projects tremendously (sp). Images created from this program can be found at http://www.cerca.umontreal.ca/vu/Welcome_eng.html. Make sure you check out the gallery at http://www.cerca.umontreal.ca/vu/gallery/Welcome_eng.html. The people behind Vu are very gratious and the program is free for those in acadamia. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 email: daizadeh@indigo.ucdavis.edu Phone: 916.754.8695 -------------------------------------------------------------------------------- Below was the problem: Hello. Would anyone know an easy-to-learn program that allows for visualizing data from a file in 3-dimension Euclidean space something that looks like a fluid dynamics simulation? I started to write such a piece of code using Tcl/Tk but speed is of the essence (as always). Thanks in advance. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 -------------------------------------------------------------------------------- #1) I use FAST, developed here, and available for free (I think). It does 3D scalar and vector fields on a wide variety of grids, including, of course, uniform cartesian. For some examples of what it can do for molecules, see http://science.nas.nasa.gov/~creon/papers/mgms96/ for availablitty of FAST, look at http://science.nas.nasa.gov/Software/FAST/ #2) Check out software at http://www.fortner.com/ I have never used their stuff, but it looks impressive (and they have been in business for a while). It is not free - but I think their main modules come as a package for less than $1,000. Fortner: http://www.fortner.com/docs/demos_all.html #3) Try pgplot. It's not available in netlib but it's excellent and free. See http://astro.caltech.edu/~tjp/pgplot/ It may not do *exactly* what you need but I think it'll come close, probably a lot closer than other free tools. #4) Sorry about the delay, but hours are not always so extensible as I might wish! Yes! VU can create pictures of 3-d fields using streamlines and/or vectors. Yes!! VU can displayed atoms and links between them using spheres and cylinders colored according to the usual standards. And Yes!!! you can put all of this on screen at the same time! We have created a couple of new images in the VU gallery representing small molecules in which a cutting plane is used to probe and visualize a scalar field. These are not big protein but rather small molecules, but the idea is the same. I invited you to go check again the VU home page at http://www.cerca.umontreal.ca/vu/gallery/ to check these new additions. VU is developped mainly for use in Computational Fluid Dynamics (CFD), but it also usefull for other application domains. It is being use extensively for chemistry applications here at Cerca and nearby universities, and also at the University of Hannover with AllChem (their web address is in VU HomePage). ** VU allows for 2-d and 3-d exploration of scalar fields as well as vector fields. Furthermore, VU can also display geometric entities such as curves and surfaces. ** Scalar fields can be probed/represented using either : - iso-surfaces in 3-d space, - iso-lines on arbitrary cutting planes - iso-lines on surfaces of constant coordinate from a structured grid. - graphs, i.e. continuously shaded images representing the values of a scalar field on cutting planes (or surfaces of constant coordinate from a structured grid). ** Vector fields can be probed/represented using either : - arrows (scalable) - streamlines in various number and location, all of which is specified interactivally. - dynamic particle tracing: non static images in which particle (represented as small spheres) are injected in various location to probe the vector fields. ** VU can extract information from these various fields and present them in a tabular form in a file or directly at the cursor location. ** VU uses `expressions' such as "sqrt(px*px+py*py+pz*pz)" to indicate color mapping, deformation or scaling factor for use in creating images (at least colorfull if not always meaningfull!). ** VU can also use transparency in any image, in order to be able able to `see' what is behind a cutting plane or an iso-surface. ** VU uses OpenGL and Motif (both fairly standard libraries) and works on UNIX workstations: IRIX, AIX, HP-UX, OSF1 and Linux. In a nutshell, VU can creates many and various images of 2-d and 3-d scalar and vector fields from a solution computed over a set of grid nodes. The input file for VU specifies the mesh used and the computed solution fields. You may see and read about some examples in the VU Web pages. However, if the fact that some of the web pages crucial for a full understanding of the capabilities of the program and of its input file might not be in english, you could forward a sample test case of your data to support_vu in order to establish its usuability in your case. Even if the documentation has not been yet completely translated and made avalailable on the Web, VU is nonetheless available in four languages: french, english, german and spanish. #5) IBM visualization data explorer/IRIS explorer will do. A while ago, i downloaded the comparison of these visualization softwares. Now I dont remember the URL. But u can find them in my homepage. http://144.16.73.100/~parthi/home.html and CLICK "visualization". u can see the comparison of four visualization softwares. #6) One possibility for almost all visualization tasks is to write a simple program to transform the data to a VRML file and then use a VRML browser to visualize it. For more information about VRML, look at the VRML repository (http://www.sdsc.edu/vrml/). For an example of code that generates VRML, look at the VRML module on my Python page (http://www.yi.com/home/HinsenKonrad/python.html). #7) I'm glad you enjoyed the site. I usually use Matlab or Mathematica to plot my vectors. Unfortunately, both of these programs are commercial so you must buy them. There may be shareware available on the internet to do the same thing. Happy hunting. #8) I don't know what your constraints are: systems, time, money, expertise ... but if I were in your position, I could knock out a visualization of "data from a file in 3-dimension Euclidean space something that looks like a fluid dynamics simulation" in 30-60 minutes using AVS. Have you any familiarity with it at all? There were other packages (IBM's Data Explorer and SGI's IRIS Explorer) which did much the same thing and were all the rage 3-4 years ago. #9) Vis5D will suit your needs if your data are sampled on a rectangular 3-D grid, and you have values for px, py and pz at each grid point. See Section 3.1 of the Vis5D README file for instructions about getting your data into Vis5D. I recommend map projection 0 (generic) and vertical coordinate system 0 (generic), since your data are not related to Earth coordinat (latitude and longitude). If you use the names 'U', 'V' and 'W' for px, py and pz then Vis5D will recognize these as the three components of a vector field. If you don't, then you can use the 'UVW VARS' widget to tell Vis5D which fields are vector components. In generic coordinates, vector components are in the units given for North, South, East, West, Top and Bottom bounds, per second. If you have a time sequence of data (i.e., a changing vector field), Vis5D will trace motion trajectories for you. You'll need to correctly assign dates and times to time steps to get realistic motions. If you only have one time step, you can still look at motion trajectories by just repeating the same data over a sequence of times. Good luck. #10) The purpose of this message is to give you a quick feeling for how the NCAR graphics package can be used to display graphs of your data from the Cray. The NCAR graphics package consists of libraries of C and Fortran callable subrou- tines for creating graphs and utilities for displaying them. #11) MSI's software developer's kit does exactly what you want. It includes an API set to visualize iso-surfaces, molecular structure, trajectories, normal modes, plots/graphs, etc. It also allows you in a few steps to put an interface together to any computational chemistry code. For general information about this toolkit visit: http://www.msi.com/support/sdk/ for specific information on plotting iso-surfaces visit: http://www.msi.com/support/sdk/users/examples/iso/README.html #12) Dear CCLers, although I'm pretty sure this question has been already posed (and I beg your pardon for posing it again), I have to ask about a 3D visualisation tool. I worked with SciAn, which is pretty good indeed, but the only existing version needs Z buffer and DGL. Looking on the net I found a software called vis5d, pretty good the same but tuned for metereological data and I found too time-expensive to adapt it to visualize orbitals, electronic density and so on. I'm using molden but I would like to find out soemthing more general (I'm trying to use ELF also, and this feature is not implemented in molden). The software I'm looking for should manage x,y,z,function_value in order to give isosurfaces of the function I'm trying to plot. Something not strictly platform-dependant would be very fine. Thank you for all the information you will provide. Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 email: daizadeh@indigo.ucdavis.edu Phone: 916.754.8695 Fax: 916.752.8995 From acidphreak69@hotmail.com Thu Jul 10 16:06:12 1997 Received: from f18.hotmail.com for acidphreak69@hotmail.com by www.ccl.net (8.8.3/950822.1) id PAA01199; Thu, 10 Jul 1997 15:34:05 -0400 (EDT) Received: (from root@localhost) by f18.hotmail.com (8.7.5/8.7.3) id MAA02491; Thu, 10 Jul 1997 12:33:34 -0700 (PDT) Message-Id: <199707101933.MAA02491@f18.hotmail.com> Received: from 206.29.126.161 by www.hotmail.com with HTTP; Thu, 10 Jul 1997 12:33:34 PDT X-Originating-IP: [206.29.126.161] From: "chris brown" To: chemistry@www.ccl.net Content-Type: text/plain Date: Thu, 10 Jul 1997 12:33:34 PDT hey you da man well send me more info _______________________________________________________ Get Private Web-Based Email Free http://www.hotmail.com From acidphreak69@hotmail.com Thu Jul 10 16:06:34 1997 Received: from f3.hotmail.com for acidphreak69@hotmail.com by www.ccl.net (8.8.3/950822.1) id PAA01205; Thu, 10 Jul 1997 15:34:45 -0400 (EDT) Received: (from root@localhost) by f3.hotmail.com (8.7.5/8.7.3) id MAA13220; Thu, 10 Jul 1997 12:34:20 -0700 (PDT) Message-Id: <199707101934.MAA13220@f3.hotmail.com> Received: from 206.29.126.161 by www.hotmail.com with HTTP; Thu, 10 Jul 1997 12:34:20 PDT X-Originating-IP: [206.29.126.161] From: "chris brown" To: CHEMISTRY@www.ccl.net Content-Type: text/plain Date: Thu, 10 Jul 1997 12:34:20 PDT hey you da man well send me more info _______________________________________________________ Get Private Web-Based Email Free http://www.hotmail.com From frenz@fs.cc.ocha.ac.jp Thu Jul 10 22:12:53 1997 Received: from fs.cc.ocha.ac.jp for frenz@fs.cc.ocha.ac.jp by www.ccl.net (8.8.3/950822.1) id VAA03598; Thu, 10 Jul 1997 21:30:34 -0400 (EDT) Received: from mozart ([133.65.49.251]) by fs.cc.ocha.ac.jp (5.x/OchaFs-R1.0.0) id AA19235; Fri, 11 Jul 1997 10:23:18 +0900 Date: Fri, 11 Jul 1997 10:23:18 +0900 Message-Id: <9707110123.AA19235@fs.cc.ocha.ac.jp> X-Sender: frenz@fs.cc.ocha.ac.jp X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: From: Franz Renz Subject: CCL:Summary: Why does G94W's SCF option make errors? 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: 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. 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 --- 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 --- ___ _ | 1 | _ \= / / \ \ =/ >---------< ( @ @ ) -------oOOo----(_)----oOOo-------------------------------------- Franz RENZ O C H A N O M I Z U University Faculty of Science, Department of Chemistry (Dr. Dipl.-Ing.) 2-1-1, Otsuka, Bunkyo-ku, Tokyo 112, JAPAN JSPS-Fellow) Tel.:+81-3-5978-5291, Fax.: +81-3-5978-5898 E-mail: frenz@fbch.tuwien.ac.at .oooO ( ) Oooo. ----------\ (----( )------------------------------------------ \_) ) / (_/