From owner-chemistry@ccl.net Tue Jun 3 05:48:00 2008 From: "Justin Finnerty justin.finnerty]-[uni-oldenburg.de" To: CCL Subject: CCL: computer for high-level QC calculations Message-Id: <-37082-080603052631-6070-2iWKLJTaer0/ttUZ/L/dVw*o*server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 03 Jun 2008 10:34:27 +0200 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty-,-uni-oldenburg.de] On Mon, 2008-06-02 at 10:58 +0200, Pablo Echenique echenique.p:gmail.com wrote: > Dear friends and colleagues, > > at my laboratory, we are about to buy a computer for performing > high-level QC calculations (e.g., coupled cluster) in biological > molecules (e.g., peptides). I write to kindly ask you for advice > regarding the "best" (in whatever sense you consider appropriate) > choice. My observations of coupled cluster calculations on our cluster are the following. Most of the the QC codes that I know cannot run totally in memory, and often require lots of disk space. We find that local scratch disk is a must; we have a 2TB NFS filesystem and have tried parallel filesystems but both are very significantly inferior to local scratch for these jobs. We have one 16cpu machine with 64Gb RAM and 2.5Tb SCSI RAID storage and find that coupled cluster calculations performance "improvement" degrades when more than 8 cpus are used and also when more than one job runs on a node. If I was in your situation my recommendation as best value for money would be a base node with: 4 or 8 cpus (eg 2 x Quadcore AMDs) 2Gb RAM/CPU (eg 16 Gb RAM) 1 system disk (only ~50 Gb is necessary) 3 x 350+ Gb sata disks as local scratch (linux soft RAID, best not to include the system disk) Set up your queue system to run only one job per node. Unless you know that the problem sizes are always the same, I would buy some nodes with smaller and some with larger scratch disk systems. This would allow you to cater to a wider range of job sizes possibly without extra cost. To upgrade the performance/capacity to this base system I would recommend first buying more nodes rather than upgrading nodes, then larger disks, then more RAM and lastly more CPUs/CPU speed. Ideally I would ask potential suppliers to provide a test machine and actually run test jobs of the size you are actually going to be doing. In particular monitor memory and disk activity. Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Tue Jun 3 07:21:01 2008 From: "Rajagopalan S. r.subramanian[a]ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: problems in Message-Id: <-37083-080603071922-25241-f41WYhYubFOFcbe0tZsNbw===server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 03 Jun 2008 13:18:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian() ipc.uni-stuttgart.de] Hi Brain, CJC, Yes my complex is high spin tetranuclear Fe catalyst. So altogether 20 electrons (hence multiplicity of 21). regards, raj Christopher Cramer cramer#%#umn.edu wrote: > There is a curious bias for low spin amongst CCL readers. > > Irrespective of whether Gaussian's FORMAT statement ever envisioned 3 > digits to the left of the decimal place in S^2, a value of 110 is > perfectly reasonable. It implies 20 unpaired electrons all high-spin > coupled ( S^2 = S * (S + 1) = 10 * 11 = 110). This is a very nice > single determinantal wave function and might be expected in the case > of, say, a tetranuclear manganese complex having 4 ferromagnetically > coupled d5 Mn ions. > > Of course, the particular input deck of Raj S might indeed have an > error, but there is nothing intrinsically wrong with the S^2 value. > Instead, the formatting issue simply reflects what is likely to be > some of the oldest (original?) code in Gaussian, written back in the > day when small organic molecules where mostly the rule... > Interestingly, the FORMAT used in the spin annihilation line is more > flexible. > > CJC > > On Jun 2, 2008, at 6:25 PM, Brian Salter-Duke > brian.james.duke[#]gmail.com wrote: > >> >> Sent to CCL by: Brian Salter-Duke [brian.james.duke]=[gmail.com] >> Raj S r.subramanian|,|ipc.uni-stuttgart.de wrote: >>> Sent to CCL by: "Raj S" [r.subramanian^ipc.uni-stuttgart.de] >>> Dear ccl users, >>> I am using Gaussian03 package for optimization and freq. >>> calculations. After opt. and freq. calculations i notice in the .log >>> file the total spin is marked ******. For e.g., look below >>> (A) (A) (A) (A) >>> of initial guess=******* >>> Requested convergence on RMS density matrix=1.00D-08 within1000 cycles. >>> Requested convergence on MAX density matrix=1.00D-06. >>> Requested convergence on energy=1.00D-06. >>> No special actions if energy rises. >>> Restarting incremental Fock formation. >>> SCF Done: E(UB+HF-LYP) = -2934.91465147 A.U. after 20 cycles >>> Convg = 0.9816D-08 -V/T = 2.0810 >>> S**2 = ******* >>> Annihilation of the first spin contaminant: >>> S**2 before annihilation 110.0343, after 110.0001 >>> 1 Symmetry operations used in ECPInt. >>> I dont know what is it *******?Is this some error... >> >> It means the number is out of bounds of the format used to print. The >> problem is 110.0343 for S**2. This is way too high. What spin state >> do you have and what S**2 would you expect for a pure spin state >> (i.e. from ROHF not UHF)? >> >> Brian. >> >>> many thanks for your reply >>> raja>> the strange characters on the top line to the === sign. You can also>> >> E-mail to subscribers: CHEMISTRY===ccl.net >> or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST===ccl.net >> or useConferences: >> http://server.ccl.net/chemistry/announcements/conferences/>> >> > > -- > > > Christopher J. Cramer > > University of Minnesota > > Department of Chemistry > > 207 Pleasant St. SE > > Minneapolis, MN 55455-0431 > > -------------------------- > > Phone: (612) 624-0859 || FAX: (612) 626-2006 > > Mobile: (952) 297-2575 > > cramer===umn.edu > > http://pollux.chem.umn.edu/~cramer > > (website includes information about the textbook "Essentials > > of Computational Chemistry: Theories and Models, 2nd Edition") > > > > -- ------------------------------------------------------ Rajagopalan Subramanian Universitaet Stuttgart, Zi-9.356, Pfaffenwaldring 55, D-70569 Stuttgart, Germany EU. tel. : +49 711 685 64464, fax : +49 711 685 64443 e-mail: r.subramanian{:}ipc.uni-stuttgart.de ------------------------------------------------------ From owner-chemistry@ccl.net Tue Jun 3 09:43:00 2008 From: "Thomas J leonard.jt]^[gmail.com" To: CCL Subject: CCL: Is there any optimum dihedral angle Message-Id: <-37084-080603052215-5099-9TmMKF1By5VFzWHVWrPAjw]*[server.ccl.net> X-Original-From: "Thomas J" Date: Tue, 3 Jun 2008 05:22:11 -0400 Sent to CCL by: "Thomas J" [leonard.jt : gmail.com] Hi CCLers, I would like to know about the optimum dihedral angle for imidazoles. At which level this imidaole will be strain free. Thanks in advance. Thomas From owner-chemistry@ccl.net Tue Jun 3 10:18:00 2008 From: "Narasimhan Loganathan narasimhan.loganathan:etu.univ-provence.fr" To: CCL Subject: CCL: Calculation of only external interactions in CBMC. Message-Id: <-37085-080603071013-24199-WLlGBxvHT6TfP8CDsCn3jw#server.ccl.net> X-Original-From: "Narasimhan Loganathan" Date: Tue, 3 Jun 2008 07:10:10 -0400 Sent to CCL by: "Narasimhan Loganathan" [narasimhan.loganathan\a/etu.univ-provence.fr] Dear users I am using CBMC techniques to calculate the potentials of the cyclic molecules. i am concerned only with the external interactions and not internal interactions. Can anyone suggest me how is it possible for me to calculate the external interactions alone avoiding internal interactions for the calculation of Rosenbluth weight. Thanking you Narasimhan Loganathan University of Provence Laboratoire Chimie Provence, UMR6264 Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 19 courriel: narasimhan.loganathan++etu.univ-provence.fr http://www.lc-provence.fr From owner-chemistry@ccl.net Tue Jun 3 10:53:01 2008 From: "Ivanka Angelova iangelova===esf.org" To: CCL Subject: CCL: ESF-EMBO Symposim on 'Protein Design and Evolution for Biocatalysis' Message-Id: <-37086-080603030556-24171-9Mn8eBeOvKthsqLZDbviHw+/-server.ccl.net> X-Original-From: "Ivanka Angelova" Date: Tue, 3 Jun 2008 03:05:52 -0400 Sent to CCL by: "Ivanka Angelova" [iangelova .. esf.org] ESF-EMBO Symposium on PROTEIN DESIGN AND EVOLUTION FOR BIOCATALYSIS Dates: 25-30 October 2008 Closing date for applications: 6 June 2008 Location: Hotel Eden Roc, Sant Feliu de Guixols, Spain Programme and applications: accessible online at www.esf.org/conferences/08255 Chair: Prof. Jiri Damborsky, Masaryk University, CZ Grants are available for young researchers to cover the conference fee and travel costs. Further information: www.esf.org/conferences/08255 or Ms. Jean Kelly (jkelly^^esf.org) Overview: The meeting will bring together internationally renowned speakers who will review the current state of knowledge in the field of protein design and evolution for biocatalysis. The symposium will be the third event in a series held in Paris (2002) and Greifswald (2006). The main objective of the 2008 meeting will be to intensify discussion and collaboration between experimentalists with theoreticians, which is needed for development of novel biocatalysts by combining directed evolution with rational protein design. The meeting will be highly interdisciplinary through the participation of speakers with various backgrounds and research interests. The lectures will span the fields of mechanistic enzymology, biocatalysis, protein crystallography, computer simulations, phylogenetics, structural bioinformatics and synthetic biology. A substantial amount of time will be devoted to poster presentations and informal discussion to promote exchange of ideas and dissemination of information. Young scientists are encouraged to actively participate and a number of lectures will be reserved for their presentations based on originality and scientific quality of submitted abstracts. From owner-chemistry@ccl.net Tue Jun 3 11:27:01 2008 From: "Mike Devereux Michael.Devereux.:.unibas.ch" To: CCL Subject: CCL:G: Morphy98 Message-Id: <-37087-080603103342-31506-kkED8Vpic2zePE35rY/hUw:-:server.ccl.net> X-Original-From: "Mike Devereux" Date: Tue, 3 Jun 2008 10:33:38 -0400 Sent to CCL by: "Mike Devereux" [Michael.Devereux(!)unibas.ch] Hi Alex, I once did something similar. The Gamess output probably contains all the necessary information, but Morphy98 was written in Fortran77 so requires exactly the right Fortran formatting. This means there's perhaps an extra / missing space somewhere when compared to the Gaussian format. The other possibility is that the Gamess output doesn't include some piece of information such as orbital energy that is not required by AIMPAC, but expected by Morphy98. If you have time it should be an easy problem to fix by getting hold of a Guassian03 format .wfn file for comparison, then using a script to reformat the Gamess version slightly... Regards, Mike > "Alex Naden anaden:fsmail.net" wrote: > > Sent to CCL by: "Alex Naden" [anaden#,#fsmail.net] > Hi, > > I am currently trying to make Morphy98 to read the .wfn file generated by Gamess UK with 'aimpac' option. On comparisson, the format of the obtained .wfn file corresponds to the Morphy98 .wfn test files with which there is no problem. However, when I try to use Gamess obtained .wfn files they seemed to be ignored by the programm. Does anyone know where I can be going wrong? > > Thank you, > > Alex > > From owner-chemistry@ccl.net Tue Jun 3 15:40:00 2008 From: "Alex Naden anaden{}fsmail.net" To: CCL Subject: CCL:G: Morphy98 Message-Id: <-37088-080603153707-16868-udWxfgeDGRMi+fPSFdCxUA : server.ccl.net> X-Original-From: "Alex Naden" Date: Tue, 3 Jun 2008 15:37:02 -0400 Sent to CCL by: "Alex Naden" [anaden]_[fsmail.net] Hi Mike, Thank you for the information. It feels better somehow knowing that someone else did something similar! I will try and look at the possible differences in the .wfn files again, in case if there is something that I have not noticed before (I have some Gaussian .wfn files). Regards, Alex