From chemistry-request@server.ccl.net Fri Jan 10 09:19:40 2003 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0AEJeD01377 for ; Fri, 10 Jan 2003 09:19:40 -0500 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.4/8.12.4) with ESMTP id h0AEJe8a009735 for ; Fri, 10 Jan 2003 09:19:40 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.4/8.12.4) with SMTP id h0AEJaDj009731; Fri, 10 Jan 2003 09:19:36 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.4/8.12.1) with ESMTP id h0AEJYsq014722; Fri, 10 Jan 2003 09:19:34 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: help about charmm Date: Fri, 10 Jan 2003 09:15:56 -0500 User-Agent: KMail/1.4.1 Cc: Rick Venable MIME-Version: 1.0 Message-Id: <200301100915.56185.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0AEJeD01378 Hi,all: I am simulating a "peptide in chloroform" system using charmm. and I want to see if one specific conformation could be kept in the simulation. so during the minimization and equilibration, I constrained the dihedral angles to keep the conformation, and before starting the dynamic run, I released the constraint and let the system go.but after about 300ps,the running was broken and charmm gave out following error message. could any body tell me what is the matter?I will attach the error message and input file. 1)input file: **************************************** ................................(omitted the psf and coordinates reading parts) !nonbond interaction options NBONDS ATOM EWALD PMEWALD KAPPA 0.32 FFTX 30 FFTY 30 FFTZ 30 ORDER 6 - CUTNB 12.0 CTOFNB 10.0 VDW VSHIFT ! impose periodic boundary conditions: set L 30.0 crystal define cubic @L @L @L 90.0 90.0 90.0 crystal build noper 0 cutoff 12.0 image byres XCEN 0.0 YCEN 0.0 ZCEN 0.0 select segid SOLV end image byres XCEN 0.0 YCEN 0.0 ZCEN 0.0 select segid ANTA end update inbfrq 1 imgfrq 1 SHAKE BONH TOLERANCE 1.0e-6 para set p e116 title * dynamics equilibration phase * ! set up output open read unit 30 card name output/@p_eq3.rst open unit 50 card write name output/@p_dyn.stt open unit 61 card write name output/@p_dyn.rst open unit 60 unfo write name output/@p_dyn.cor open unit 62 unfo write name output/@p_dyn.vel ! heat system by MD : assign velocities from Gaussian distribution ! at progeressively higher temepratures DYNAMICS LEAP VERLET RESTART NSTEP 1000000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 5000 - KUNIT 50 IUNWRI 61 IUNREAD 30 IUNCRD 60 IUNVEL 62 - imgfrq 25 inbfrq 25 ihbfrq 0 - NPRINT 100 NSAVC 10 NSAVV 10 open write card unit 11 name crd/e116_dyn.pdb write coor pdb card unit 11 close unit 11 OPEN UNIT 38 CARD WRITE NAME crd/e116_dyn.crd WRITE COOR CARD UNIT 38 CLOSE UNIT 38 stop *************************************************************** 2)error message: **************************************************8 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 0 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -118.6741615914 RRPR= -3.0523892808 X(I) -1.0072591014 1.3202935338 -1.3045016708 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.8531869062 0.4484378605 -12.2079093966 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 1 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -29.4221023014 RRPR= -1.5388717892 X(I) -1.0021304050 1.2912715351 -1.6674501432 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.9244544165 0.8517227173 -7.1644379164 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 2 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -7.1151444645 RRPR= -0.7945813248 X(I) -0.9996083068 1.2769996176 -1.8459344280 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.9595010735 1.0500429052 -4.6842500420 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 3 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -1.5607449339 RRPR= -0.4459900113 X(I) -0.9984270723 1.2703153099 -1.9295282321 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.9759153106 1.1429269312 -3.5226444725 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 4 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -0.2383717583 RRPR= -0.3097583685 X(I) -0.9979654386 1.2677030410 -1.9621972081 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.9823300961 1.1792265834 -3.0686818265 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 5 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -0.0115266923 RRPR= -0.2798010496 X(I) -0.9978639254 1.2671286035 -1.9693811113 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.9837407065 1.1872088718 -2.9688555049 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE NITER= 6 LL= 24 I= 45 J= 46 TOLER= 0.9940090000 DIFF= -0.0000330333 RRPR= -0.2781973369 X(I) -0.9978584911 1.2670978520 -1.9697656890 XREF(I) -0.1732638907 1.1171361155 -12.5019766435 X(J) -0.9838162211 1.1876361896 -2.9635114775 XREF(J) -0.8449202314 0.4550922027 -12.1785811928 TOTAL ENERGY CHANGE EXCEEDED 20. KCAL AND 10% OF THE TOTAL KINETIC ENERGY IN THE LAST STEP PREVIOUS E = 542.1 CURRENT E = 0.1297E+07 KINETIC = 0.5518E+07 WRIDYN: RESTart file was written at step 800176 ***** LEVEL -2 WARNING FROM ***** ***** ENERGY CHANGE TOLERANCE EXCEEDED ****************************************** BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5 ************************************************************************************************************** From chemistry-request@server.ccl.net Fri Jan 10 10:19:17 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0AFJHD03160 for ; Fri, 10 Jan 2003 10:19:17 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0AFJHj01341; Fri, 10 Jan 2003 10:19:17 -0500 (EST) Date: Fri, 10 Jan 2003 10:19:15 -0500 (EST) From: Jan Labanowski To: chemistry@CCL.net cc: jkl@ccl.net, Steven.Trohalaki@wpafb.af.mil Subject: Letters to support my nomination for Patterson-Crane Award Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, First, I would like to thank Steven for nominating me to the prestigious Patterson-Crane Award award. It makes me feel honored and gives me a boost to continue. While you may consider it shameless that I am asking for support, be pragmatic about it. This award would REALLY help CCL !!!. It needs recognition to continue and prosper. So when you send your support letters to Steve, do not think much about my humble person, but about us, about the community which CCL created. Say what CCL brings for us all, and why it is worthwhile. Thank you again for your help... Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ > Dear CCLers, > > I am nominating Jan Labanowski for ACS's Patterson-Crane Award > (see http://membership.acs.org/C/Colu/welcome.html ) and I am in need of > seconding letters. There is no limit and the Chair of the awards committee > says that the more supporting material the better so I'd be obliged if you > would send me email with a statement on what CCL means to you and how > it's helped your career. > > Sincerely, > > Steve Trohalaki > Visiting Scientist > Air Force Research Lab > steven.trohalaki@wpafb.af.mil From chemistry-request@server.ccl.net Fri Jan 10 10:01:15 2003 Received: from huygens.rijnh.nl ([192.42.124.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0AF1ED02403 for ; Fri, 10 Jan 2003 10:01:14 -0500 Received: from [192.42.124.115] (macgvh.rijnh.nl [192.42.124.115]) by huygens.rijnh.nl (SGI-8.9.3/8.9.3) with ESMTP id QAA88949 for ; Fri, 10 Jan 2003 16:02:39 +0100 (MET) Mime-Version: 1.0 X-Sender: gertvh@huygens.rijnh.nl Message-Id: In-Reply-To: References: Date: Fri, 10 Jan 2003 16:01:57 +0100 To: From: Gert von Helden Subject: Re: CCL:Fast PyMOL (and other 3D progs.) on OSX Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hello, I just compiled viewmol 2.3 on my Mac. Very nice to, for example, animate vibrations from gaussian or gamess. The program runs very nice and fast. It compiled after a few adaptations. E-mail me if you want to know details. Greetings, Gert At 17:28 -0800 8/1/03, DeLano, Warren wrote: >Good news for OSX users -- the Mac can finally do fast OpenGL >graphics under X11! > >With OSX 10.2.3, the public X11 beta, and Fink, you can now install >a complete version of PyMOL on a Mac without compromising >performance. The same should be true for most of your other >favorite X11/OpenGL graphics programs. > >You can find two sets of instructions on how to do this linked from >the PyMOL home page. > >http://pymol.sf.net > >Cheers, >Warren > -- ******************************************************* Gert von Helden FOM Institute for Plasmaphysics Rijnhuizen Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands http://www.rijnh.nl/ e-mail: gertvh@rijnh.nl phone: (+31) 30 6096999, fax: (+31) 30 6031204 From chemistry-request@server.ccl.net Mon Dec 23 15:07:20 2002 Received: from api_lab_bdc.achillion.com ([64.51.60.221]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBNK7Jh23007 for ; Mon, 23 Dec 2002 15:07:20 -0500 Received: by api_lab_bdc.achillion.com with Internet Mail Service (5.5.2653.19) id ; Mon, 23 Dec 2002 15:05:26 -0500 Message-ID: From: Ken Torikoshi To: "'chemistry@ccl.net'" Subject: Alternative DBs for WDI and MDDR? Date: Mon, 23 Dec 2002 15:04:56 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi All, We are looking for any (free if possible) alternative databases for WDI and MDDR for our computational analysis. Does anyone have any information. Please let us know. We will summarize the results. Thank you. -- Ken ---------- Kenichi Torikoshi ktorikoshi@achillion.com From chemistry-request@server.ccl.net Fri Jan 10 11:51:40 2003 Received: from albert.unito.it ([130.192.119.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0AGpeD05918 for ; Fri, 10 Jan 2003 11:51:40 -0500 Received: (from root@localhost) by albert.unito.it (8.12.2/8.12.2) id h0AGpZtU006077; Fri, 10 Jan 2003 17:51:35 +0100 Received: from unito.it (chpc28.ch.unito.it [130.192.118.37]) by albert.unito.it (8.12.2/8.12.2) with ESMTP id h0AGpZDn006036; Fri, 10 Jan 2003 17:51:35 +0100 Message-ID: <3E1EFA42.2FE64BA2@unito.it> Date: Fri, 10 Jan 2003 17:52:18 +0100 From: MSSC Organization: Dip. Chimica IFM X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: MSSC2003 - Ab initio Modeling in Solid State Chemistry X-scanner: scanned by Inflex 1.0.9 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit International School of Advanced Study of the University of Torino Ab initio Modeling in Solid State Chemistry MSSC2003 http://www.chimifm.unito.it/teorica/mssc2003 September 7-12, 2003 - Torino, Italy Director: R. Dovesi, University of Torino The Theoretical Chemistry Group of the Torino University is organizing a new edition of the Summer School on the ab initio simulation of crystalline and defective solids. The school is addressed to PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis and will provide an overview of the possibilities offered by ab initio quantum mechanical techniques when applied to characterize solid state materials. The new capabilities of CRYSTAL03 will be illustrated. Outline of the subjects + Introductory lectures: - Space groups and point symmetry - Reciprocal space and Bloch functions - Hamiltonians and Basis sets + The structure of the CRYSTAL code: basis set, hamiltonians, accuracy. + Total energy and related quantities: equations of state, solid state reactions, phase transitions. + Geometry optimization: strategies and techniques. + One electron properties: DOS, band structure, charge and spin density maps, electrostatic potential + Localized crystalline orbitals - Wannier Functions. + Dielectric properties: dielectric and piezoelectric tensors; spontaneous polarization through the Berry phase and Wannier functions. + Spin polarized solutions: ferromagnetism and antiferromagnetism, Fermi contact and hyperfine coupling constants. + Surface chemistry and heterogeneous catalysis: models, accuracy and limitations. + Local defects in solids: the observables of interest; the possible strategies. + Post-HF ab initio techniques for crystals Program The school will last six days (7-12 September 2003) and will be held at the Chemistry Departments of the Torino University. The morning sessions will be devoted to lectures by experts. The afternoons will be dedicated to practical sessions. In the tutorials it will be shown how to obtain information concerning various observables using the CRYSTAL code. There will be the possibility to present posters, that will be on display for the whole school and discussed during a special session. Participation is limited to 40 people. Accommodation will be at the University Guest House, in double rooms. The total cost of the school is expected to be 500.00 Euro. A small number of bursaries will be available, to cover the participation fee of researchers from less favourite countries. Teachers The local staff of the Theoretical Chemistry Group (R. Dovesi, C. Pisani, C. Roetti, P. Ugliengo, S. Casassa, A.M. Ferrari, B. Civalleri, G. Capecchi, F. Lopez, A. Damin, G. Mallia, F. Pascale from Torino University and R. Orlando > from the University of Eastern Piedmont) will be supported by highly qualified European scientists, including: M. Catti, Università di Milano Bicocca (Milano) - Italy F. Corà, The Royal Institution (London) - U.K. Ph. D'Arco, Université P. et M. Curie (Paris) - France R. Resta, SISSA (Trieste) - Italy N. M. Harrison, CLRC and Imperial College - U.K. V. R. Saunders, CLRC Daresbury Laboratory - U.K. A. Savin, Université P. et M. Curie (Paris) - France C. M. Zicovich Wilson (Cuernavaca) - Mexico K. Doll, University of Braunschweig - Germany Y. Noel, Université P. et M. Curie (Paris) - France M. Llunell, University of Barcelona - Spain I.P.R. de Moreira, University of Barcelona - Spain Deadlines and Contact Information: II circular and application form: March 15th Submission of application form: May 1st Notification of acceptance: May 15th Submission of poster abstracts: July 15th E-mail mssc@unito.it Telephone: +39 011 670 7564 Fax: +39 011 670 7855 Postal address: MSSC2003 - Dipartimento di Chimica IFM Via Giuria 5 - I 10125 Torino Italy _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex