From owner-chemistry@ccl.net Thu Jan 14 08:58:01 2010 From: "Jiyoung Cha jycha04,gmail.com" To: CCL Subject: CCL: Recently Status of Computational Chemisty Tools Message-Id: <-41044-100113215133-8837-lh9FDXCUFRGoU9H75lzgPA]_[server.ccl.net> X-Original-From: "Jiyoung Cha" Date: Wed, 13 Jan 2010 21:51:29 -0500 Sent to CCL by: "Jiyoung Cha" [jycha04^gmail.com] I am suveying present status of grid-based computational chemistry tools. What is the most commonly used tools, I wonder if any research is the most used it. If you have been anaylzed statistical data, I want to provide them. Thank you for reading and have a nice day! From owner-chemistry@ccl.net Thu Jan 14 09:33:01 2010 From: "Rene thomsen rt,+,molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Molecular Viewer 2.0 Message-Id: <-41045-100114014114-32389-2q6OkDNDGgVgGsaitoS4gw[a]server.ccl.net> X-Original-From: "Rene thomsen" Date: Thu, 14 Jan 2010 01:41:10 -0500 Sent to CCL by: "Rene thomsen" [rt _ molegro.com] Aarhus, Denmark, January 14th, 2010 - Molegro is pleased to announce a new major release of Molegro Molecular Viewer, a free cross-platform application for visualization of molecules and Molegro Virtual Docker results. Molegro Molecular Viewer offers a high-quality visualization tool combined with a user interface experience focusing on usability and productivity. Highlights of Molegro Molecular Viewer: * Share and view results from Molegro Virtual Docker docking runs. * Imports and exports PDB, SDF, Mol2, and MVDML files. * Automatic preparation of molecules. * Molecular surface and backbone visualization. * Labels, sequence viewer, and biomolecule generator. * Cropping of molecules and clipping planes. * Structural protein alignment. * Cross-platform: Windows, Linux, and Mac OS X is supported. New features in version 2.0: * A new built-in raytracer making it possible to create publication quality graphics. * Support for reading Molegro Virtual Docker version 4.0 MVDML files. * Improved molecular surface and 'tube' backbone rendering. * Wireframe view now shows double, tripple, and delocalized bonds. * Minor user interface improvements and bug fixes. To download Molegro Molecular Viewer, please visit our company website at: http://www.molegro.com For more information contact: Rene Thomsen, CEO Molegro C. F. Moellers Alle 8, Bldg. 1110 DK-8000 Aarhus Denmark E-mail: rt^-^molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Thu Jan 14 11:06:00 2010 From: "Giuseppina Gini gini:-:elet.polimi.it" To: CCL Subject: CCL: Recently Status of Computational Chemisty Tools Message-Id: <-41046-100114104246-24043-BxcFXkHlxfRv3ltCuBHs6g{:}server.ccl.net> X-Original-From: "Giuseppina Gini" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8;format="flowed" Date: Thu, 14 Jan 2010 15:51:24 +0100 MIME-Version: 1.0 Sent to CCL by: "Giuseppina Gini" [gini[a]elet.polimi.it] you can have a look at an European project (Chemomentum) about using UNICORE for chemistry http://www.fz-juelich.de/jsc/grid/Chemomentum Giuseppina Gini On Wed, 13 Jan 2010 21:51:29 -0500 "Jiyoung Cha jycha04,gmail.com" wrote: > > Sent to CCL by: "Jiyoung Cha" [jycha04^gmail.com] > I am suveying present status of grid-based computational >chemistry tools. > > What is the most commonly used tools, I wonder if any >research is the most > used it. > > If you have been anaylzed statistical data, I want to >provide them. > > Thank you for reading and have a nice day! > > > > -= This is automatically added to each message by the >mailing script =- > To recover the email address of the author of the >message, please change > the strange characters on the top line to the * sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST * ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > From owner-chemistry@ccl.net Thu Jan 14 14:20:00 2010 From: "Rudolf Herrmann rudolf.herrmann]-[physik.uni-augsburg.de" To: CCL Subject: CCL: GAMESS:SCF-Problem with DFT Message-Id: <-41047-100114121607-28415-ZiG9xF7F017tb6EqKOvUcQ()server.ccl.net> X-Original-From: "Rudolf Herrmann" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 14 Jan 2010 18:15:52 +0100 MIME-Version: 1.0 Sent to CCL by: "Rudolf Herrmann" [rudolf.herrmann#,#physik.uni-augsburg.de] Dear Gustavo, thank you for your suggestions. I played some time around with the options, and finally got it work. > > Sent to CCL by: Gustavo Mercier [gamercier::yahoo.com] > Hi! > > Several points: > > 1. Normally if you go with DIIS then Damping and Vshifting is turned off. > Look at the REF.doc in the Gamess distribution where they give hints > for helping in convergence. OK I know that. Damping and Vshifting is there only in case DIIS does not start immediately. > They also make a suggestion in the INPUT.doc > under the SCF namelist where they suggest using ETHRESH and > SWDIIS. I do not recommend the SWDIIS option because what it does is > switch from DIIS to the second order method (SOSCF), and this has not > worked out as well for me. > That's precisely what I found as well: SOSCF is much more sensitive and crashes easier than DIIS. > 2. Set ETHRESH (option under SCF) to a large value like 2E+0. This will > make DIIS kick in early, and should stay on pretty much all the time. > That was precisely what worked! Although DIIS was switched off again once, SCF did recover after ca. 30 crazy steps and finally converged. > 3. Another thing is the number of points used for computing the functional > integrals. This is done numerically and is controled by the DFT namelist. > The program uses a low number of points in the early iterations, and then > switches to the full grid. I find that I have to start the full grid > earlier. That was not successful in my case. > I've also had to use larger than default values and go up to 434 > and 590. I do work on Mn coordination complexes and they seem to be fairly > soft with a fairly flat potential energy curve. Read under REF.doc details > about the grids and expected accuracy in the energy gradients. > Together with ETHRSH=2.0 this works as well but does not really improve the calculation. > I would also recommend doing the geometry optimization with delocalized > coordinates: > > $ZMAT DELOC=.T. AUTO=.T. $END > > you also need to specify the number of variables in the $CONTRL namelist > using (I believe) NZVAR=3*N-6 where N is the number of atoms. > This will reduce the number of iterations and I find that it makes for a > smarter optimization. Did not work (I tried that with isomers of this compound earlier as well). The program crashes with BAD DELOCALIZED COORDINATES GENERATED !!! > > On another note... if you intend to do thermochemistry, I've found that > the 'approximate' hessian kicked out at the end of the geometry > optimization is not bad. For DFT the second derivatives are computed using > numerical methods from (mostly) analytic gradients. Seems tha the > augmented hessian methods that are used for default in geometry > optimizations do a good job at getting the hessian ok, or at least as good > as the default one-point numerical differentiation formula. > Thanks a lot for this hint. Actually I do not need thermochemistry for the moment, but that could be very helpful for the future. > Hope this helps! > > -- > Gustavo A. Mercier, Jr., MD, PhD > gamercier=yahoo.com > Gustavo.Mercier=bmc.org > gumercie=bu.edu > 617-414-6440 > Thank you again Yours Rudolf. > > > > ----- Original Message ---- >> From: Rudolf Herrmann rudolf.herrmann__physik.uni-augsburg.de >> >> To: "Mercier, Gustavo, " >> Sent: Mon, December 21, 2009 6:42:44 AM >> Subject: CCL: GAMESS:SCF-Problem with DFT >> >> >> Sent to CCL by: "Rudolf Herrmann" >> [rudolf.herrmann:+:physik.uni-augsburg.de] >> Hello all, >> I'm using GAMESS(US), rev. R3 from Jan 12, 2009. I encountered a problem >> in obtaining SCF with DFT. Part of the input: >> >> $CONTRL SCFTYP=UHF MULT=2 RUNTYP=Optimize COORD=unique INTTYP=HONDO $END >> $CONTRL DFTTYP=PBE0 MAXIT=200 ICHARG=0 ECP=SBKJC $END >> $SYSTEM TIMLIM=80000 MEMORY=80000000 $END >> $SCF DIRSCF=.T. DAMP=.T. SHIFT=.T. DIIS=.T. SOSCF=.F. $END >> $BASIS GBASIS=SBKJC $END >> $STATPT OPTTOL=0.0001 NSTEP=200 $END >> $GUESS GUESS=HUCKEL $END >> $DATA >> 4*Fuenfring - Phthalo cctt als Cu-Komplex UHF >> C1 >> C 6.0 -5.216897 -0.910406 -10.919197 >> ....... (many atoms) >> >> And that is the result of the first SCF calculation: >> >> >> >> NONZERO >> >> >> >> >> BLOCKS >> ITER EX TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR >> VIR. SHIFT DAMPING INTEGRALS SKIPPED >> 1 0 -1036.5378101022 -1036.5378101022 1.230919053 0.821519137 >> 0.000000000 1.000000000 6231081460 193615138 >> * * * INITIATING DIIS PROCEDURE * * * >> 2 1 -1041.6461370603 -5.1083269581 11.464555047 0.402615779 >> 0.000000000 1.000000000 6236128017 193099683 >> 3 2 -1002.7358262561 38.9103108042 11.474994560 1.302218004 >> 0.000000000 1.000000000 6241249413 191679251 >> 4 3 -1041.8568160646 -39.1209898086 0.195994971 0.402579497 >> 0.000000000 1.000000000 6237469221 191939968 >> 5 4 -1042.3054537170 -0.4486376523 0.226115870 0.343346341 >> 0.000000000 1.000000000 6057043846 201451242 >> 6 5 -1042.6171017767 -0.3116480597 0.279322397 0.266341119 >> 0.000000000 1.000000000 6061097833 201455155 >> 7 6 -1042.9966679031 -0.3795661264 0.106460306 0.081821934 >> 0.000000000 1.000000000 6077977863 201147673 >> 8 7 -1043.0591297051 -0.0624618020 0.046857045 0.011477052 >> 0.000000000 1.000000000 5989046608 202974307 >> 9 8 -1043.0669450821 -0.0078153770 0.011381853 0.005948448 >> 0.000000000 1.000000000 5736168713 207005748 >> 10 9 -1043.0697884590 -0.0028433770 0.013485505 0.004417363 >> 0.000000000 1.000000000 5475629752 210127430 >> 11 10 -1043.0723408038 -0.0025523448 0.017067266 0.003869563 >> 0.000000000 1.000000000 5458702402 210313186 >> 12 11 -1043.0751463423 -0.0028055385 0.014434645 0.003675831 >> 0.000000000 1.000000000 5453595333 210460303 >> 13 12 -1043.0777030610 -0.0025567187 0.019791837 0.003849315 >> 0.000000000 1.000000000 5397573182 211084337 >> 14 13 -1043.0813673308 -0.0036642698 0.004903916 0.004281832 >> 0.000000000 1.000000000 5491928111 210122347 >> CONVERGED TO SWOFF, SO DFT CALCULATION IS NOW SWITCHED ON. >> * * * INITIATING DIIS PROCEDURE * * * >> 15 14 -1058.1568375748 -15.0754702440 1.625183076 0.052558260 >> 6225076316 194161508 >> 16 15 -1056.2538409178 1.9029966571 0.866868728 0.796456193 >> 6203667374 195873448 >> 17 16 -1058.5031727428 -2.2493318250 0.157468336 0.035593489 >> 6097769151 200991564 >> 18 17 -1058.2872778511 0.2158948917 0.070399380 0.134520819 >> 6058543947 201342138 >> 19 18 -1058.5442781186 -0.2570002675 0.113766853 0.013742123 >> 5927217989 204237218 >> 20 19 -1058.5522842356 -0.0080061170 0.023549798 0.007512045 >> 5840741652 205391057 >> 21 20 -1058.5530282008 -0.0007439652 0.017420717 0.010226036 >> 5670929315 208075365 >> 22 21 -1058.5559993807 -0.0029711799 0.047523393 0.009589402 >> 5564367770 209481859 >> 23 22 -1058.5585808178 -0.0025814371 0.029346400 0.024600824 >> 5707543406 207871809 >> 24 23 -1058.5575623133 0.0010185045 0.013103014 0.017673475 >> 5514532287 210353312 >> NEXT ENERGY RISES: SWITCHING DIIS OFF FOR 5 ITERS, NEW ETHRSH= 1.59E-02 >> 25 24 -1058.5566503140 0.0009119993 0.065560927 0.026774000 >> 5383825524 211393480 >> 26 25 -1058.5245291667 0.0321211473 0.955346110 0.097075114 >> 5824682851 206204169 >> 27 26 -1045.4354021475 13.0891270192 19.549841437 1.414811739 >> 6176465140 198256544 >> 28 27 -820.5152084492 224.9201936983 183.173769694 2.570654172 >> 6246989834 190654722 >> 29 28 615.6159645678 1436.13117301703000.606626971 2.010533226 >> 6254865291 185798793 >> 30 29 1752.6067873608 1136.99082279303001.172518613 10.378186893 >> 6256392203 177999716 >> 31 30 1765.6511795332 13.04439217243095.179109875 2.823919783 >> 6256414149 176971112 >> 32 31 2820.6124946084 1054.96131507523095.984312651 2.819419434 >> 6256313973 177970697 >> 33 32 2012.2921032636 -808.32039134473958.491129374 3.341335928 >> 6256340795 177974590 >> 34 33 3111.0312907781 1098.73918751453958.190267766 2.732484925 >> 6256322037 177808512 >> 35 34 2059.9131221528 -1051.11816862534124.537686577 3.295129177 >> 6256330123 177699772 >> ....... and so on (oscillates). >> >> My question is: Everything seems reasonable until the program's decision >> to turn off DIIS for five iterations. How can I switch off this >> behaviour? >> I did not find any hint in the manual (maybe I have simply overlooked >> it). >> >> Thanks a lot for suggestions. >> >> Merry Christmas and lots of successful calculations in the New Year! >> >> R. Herrmann. >> >> -- >> Dr. Rudolf Herrmann >> Institut für Physik >> Universität Augsburg >> Universitätsstr. 1 >> D-86159 Augsburg>> the strange characters on the top line to the = sign. You can also>> >> E-mail to subscribers: CHEMISTRYÌl.net or use:> > >