From owner-chemistry@ccl.net Wed Jan 30 00:52:00 2013 From: "alireza zeinalinezhad ar.zeinali ~~ yahoo.com" <owner-chemistry..server.ccl.net> To: CCL Subject: CCL: Forces between atoms in molecule Message-Id: <-48154-130129231956-25641-FyqayjRfRq1Yqh9niBr6dQ..server.ccl.net> X-Original-From: "alireza zeinalinezhad" <ar.zeinali\a/yahoo.com> Date: Tue, 29 Jan 2013 23:19:55 -0500 Sent to CCL by: "alireza zeinalinezhad" [ar.zeinali||yahoo.com] Dear ccl-netters, Does anyone know how to find/print the forces between atoms in molecule/cluster using g09. thank you Alireza From owner-chemistry@ccl.net Wed Jan 30 04:30:00 2013 From: "Mariusz Radon mariusz.radon . gmail.com" <owner-chemistry**server.ccl.net> To: CCL Subject: CCL: Forces between atoms in molecule Message-Id: <-48155-130130042901-3172-50i9TPnimS6dO33TYRjcxg**server.ccl.net> X-Original-From: Mariusz Radon <mariusz.radon*|*gmail.com> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 30 Jan 2013 10:28:43 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon[]gmail.com] On 30.01.2013 05:19, alireza zeinalinezhad ar.zeinali ~~ yahoo.com wrote: > Sent to CCL by: "alireza zeinalinezhad" [ar.zeinali||yahoo.com] > Dear ccl-netters, > Does anyone know how to find/print the forces between atoms in molecule/cluster using g09. > thank you > Alireza Hi Alireza: In order to obtain forces acting on the atoms you can use a small trick: just do a single step of geometry optimization, i.e., Opt(MaxCycles=1). The forces would be zero, of course, in the equilibrium geometry. However, to calculate forces acting on atoms is not really the same as to calculate "forces between atoms in a molecule/cluster." If I understood you correctly, I am afraid that what you want to obtain cannot be uniquely defined because the total energy in quantum chemistry is _not_ a pairwise inter-atomic potential. Thus, I believe it is not straightforward to decompose the resulting forces into a sum of contributions, one from each pair of atoms. Regards, Mariusz Radon> > -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Wed Jan 30 08:54:00 2013 From: "Jamie Platts Platts*_*cardiff.ac.uk" <owner-chemistry(~)server.ccl.net> To: CCL Subject: CCL: Call for nominations: MGMS Silver Jubilee Prize Message-Id: <-48156-130130051134-22855-cJ33iu7WORPfWEq0nbDjDQ(~)server.ccl.net> X-Original-From: Jamie Platts <Platts-x-cardiff.ac.uk> Content-Type: multipart/alternative; boundary="=_alternative 0037F82780257B03_=" Date: Wed, 30 Jan 2013 10:11:19 +0000 MIME-Version: 1.0 Sent to CCL by: Jamie Platts [Platts|,|cardiff.ac.uk] This is a multipart message in MIME format. --=_alternative 0037F82780257B03_= Content-Type: text/plain; charset="US-ASCII" Call for Nominations: MGMS Silver Jubilee Prize To support postdoctoral and young independent researchers, and to recognise our Silver Jubilee, MGMS has established a Silver Jubilee Prize, awarded to outstanding young researchers in the field. Previous winners include Dr. Nick Besley, Dr. Graeme Day, Dr. Cherif Matta, Dr. Andreas Bender and Dr. Marcel Swart. Nominations are now sought for the 2013 Prize, which should be submitted to Membership Secretary, Dr. James Platts (Platts(_)Cardiff.ac.uk). The closing date is April 12th 2013. All aspects of each candidate's contributions to the field of molecular modelling and related areas (covering computational molecular science, including the development of methods, scientific hypotheses and insights, research presentations, patents, software and algorithms) may be considered by the Award Committee. Purpose: The purpose of the MGMS Silver Jubilee Prize is to benefit the field of molecular modelling and its research community, and in particular to support young researchers in the field and to increase recognition of MGMS. There are currently very few prizes for young molecular modellers, compared to many awards for more 'traditional' physical chemistry. Eligibility: Researchers (in academia or industry, with or without permanent positions) in molecular modelling, simulation and visualization, with up to 10 years of postdoctoral experience. Nominees should have no more than 10 years of postdoctoral experience at the closing date. Exceptions due to career breaks may also be considered at the discretion of the Award Committee (any such circumstances should be made clear in the application). Prize: A prize of GBP500 and a commemorative medal will be awarded to the successful candidate at the discretion of MGMS (if applications of high enough quality are not received, MGMS may decide not to award the Prize in any given year). Nominations: Candidates can be nominated by others or by themselves. An application should consist of: 1. A covering letter nominating the candidate (self-nominations are accepted). 2. A two-page c.v. of the nominee, including the date of award of their PhD. 3. A list of the nominee's publications and other research outputs, with the five most important indicated by asterisks. A very short (one short paragraph maximum) description of the importance of each of these five pieces of work should be given. 4. A one-page statement from the candidate of his/her achievements and the purposes of their research. 5. Supporting statements from two referees are also required: the nominator or candidate should arrange for the referees' statements to be sent directly to the MGMS Membership Secretary. Complete applications should be sent to the Membership Secretary of MGMS, and may be sent electronically. It is the responsibility of the applicant to ensure that all relevant documents are sent to the Secretary by the required date. Criteria: The Award Panel shall decide the Award based on their assessment of the contribution of the candidate to the field of molecular modelling, molecular simulation and molecular graphics (all relevant areas of molecular modelling and related fields); these include the impact of their work; and the potential of the candidate to make further such contributions. This judgement shall be based on published work (articles in refereed journals, books and other publications) and also on other contributions such as computer software, databases and associated technology of benefit to molecular modellers; other indicators of esteem in the research community (research seminars and conference presentations; other awards; participation in the activities of MGMS and other learned societies); activities in publicizing molecular modelling, in increasing public awareness and understanding of the field, and in related education; the recommendations of the Referees; and patents or other related research outputs in molecular modelling. --=_alternative 0037F82780257B03_= Content-Type: text/html; charset="US-ASCII" <br><font size=2 face="sans-serif">Call for Nominations: MGMS Silver Jubilee Prize </font> <br> <br><font size=2 face="sans-serif">To support postdoctoral and young independent researchers, and to recognise our Silver Jubilee, MGMS has established a Silver Jubilee Prize, awarded to outstanding young researchers in the field. Previous winners include Dr. Nick Besley, Dr. Graeme Day, Dr. Cherif Matta, Dr. Andreas Bender and Dr. Marcel Swart. </font> <br> <br><font size=2 face="sans-serif">Nominations are now sought for the 2013 Prize, which should be submitted to Membership Secretary, Dr. James Platts (Platts(_)Cardiff.ac.uk). The closing date is April 12th 2013. All aspects of each candidate's contributions to the field of molecular modelling and related areas (covering computational molecular science, including the development of methods, scientific hypotheses and insights, research presentations, patents, software and algorithms) may be considered by the Award Committee. </font> <br> <br><font size=2 face="sans-serif">Purpose: The purpose of the MGMS Silver Jubilee Prize is to benefit the field of molecular modelling and its research community, and in particular to support young researchers in the field and to increase recognition of MGMS. There are currently very few prizes for young molecular modellers, compared to many awards for more 'traditional' physical chemistry. </font> <br> <br><font size=2 face="sans-serif">Eligibility: Researchers (in academia or industry, with or without permanent positions) in molecular modelling, simulation and visualization, with up to 10 years of postdoctoral experience. Nominees should have no more than 10 years of postdoctoral experience at the closing date. Exceptions due to career breaks may also be considered at the discretion of the Award Committee (any such circumstances should be made clear in the application). </font> <br> <br><font size=2 face="sans-serif">Prize: A prize of GBP500 and a commemorative medal will be awarded to the successful candidate at the discretion of MGMS (if applications of high enough quality are not received, MGMS may decide not to award the Prize in any given year). </font> <br> <br><font size=2 face="sans-serif">Nominations: Candidates can be nominated by others or by themselves. An application should consist of:</font> <br> <br><font size=2 face="sans-serif">1. A covering letter nominating the candidate (self-nominations are accepted).</font> <br><font size=2 face="sans-serif">2. A two-page c.v. of the nominee, including the date of award of their PhD.</font> <br><font size=2 face="sans-serif">3. A list of the nominee's publications and other research outputs, with the five most important indicated by asterisks. A very short (one short paragraph maximum) description of the importance of each of these five pieces of work should be given.</font> <br><font size=2 face="sans-serif">4. A one-page statement from the candidate of his/her achievements and the purposes of their research. </font> <br><font size=2 face="sans-serif">5. Supporting statements from two referees are also required: the nominator or candidate should arrange for the referees' statements to be sent directly to the MGMS Membership Secretary. </font> <br> <br><font size=2 face="sans-serif">Complete applications should be sent to the Membership Secretary of MGMS, and may be sent electronically. It is the responsibility of the applicant to ensure that all relevant documents are sent to the Secretary by the required date. </font> <br> <br><font size=2 face="sans-serif">Criteria: The Award Panel shall decide the Award based on their assessment of the contribution of the candidate to the field of molecular modelling, molecular simulation and molecular graphics (all relevant areas of molecular modelling and related fields); these include the impact of their work; and the potential of the candidate to make further such contributions. This judgement shall be based on published work (articles in refereed journals, books and other publications) and also on other contributions such as computer software, databases and associated technology of benefit to molecular modellers; other indicators of esteem in the research community (research seminars and conference presentations; other awards; participation in the activities of MGMS and other learned societies); activities in publicizing molecular modelling, in increasing public awareness and understanding of the field, and in related education; the recommendations of the Referees; and patents or other related research outputs in molecular modelling. </font> <br> --=_alternative 0037F82780257B03_=-- From owner-chemistry@ccl.net Wed Jan 30 11:59:00 2013 From: "Errol Lewars elewars- -trentu.ca" <owner-chemistry^server.ccl.net> To: CCL Subject: CCL:G: Facing difficulty in running g03 peogramm Message-Id: <-48157-130130095716-14362-kepWK1I8SItPhOMRcYy/YA^server.ccl.net> X-Original-From: Errol Lewars <elewars-*-trentu.ca> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 30 Jan 2013 09:57:20 -0500 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars%%trentu.ca] 2013 Jan 30 First, does your system calculate anything faster than a "very long time"? I found that on an aging computer the parent coumarin (C9H6O2, 11 heayy atoms--a quick indication of "size") took 7 minutes for a HF/6-31G* and 8 minutes for a B3LYP/6-31G* opt/freq. Second, the time for a job depends heavily on the method (HF, DFT and the functional, MP2, CCSD(T), etc., etc.) and the basis set (6-31G*, 6-311+G**, etc., etc.). You might start with a modest method/basis like HF/6-31G* and expect the time to rise steeply with significant increases in the computational level. And of course you have to decide from the literature or your experimentation what accuracy in dipole moment you need. E.Lewars == Mehboob Alam mehboob.cu(~)gmail.com wrote: > Hi Manjunath Wari, > > I'll suggest that you to use all the processors present in your CPU > (eg. for quadcore system you can use %nprocshared=4 as the first line > of your input). And if you are running parallel then use lindaworkers > to call several (available) nodes for your job. It will surely > increase the speed of your calculations. %nprocshared keyword can be > used for both serial and parallel jobs. > > Hope it will help. > > With best regards, > Mehboob > > On Tue, Jan 29, 2013 at 7:44 PM, Gkourmpis, Thomas > Thomas.Gkourmpis,borealisgroup.com <http://borealisgroup.com> > <owner-chemistry.:.ccl.net <mailto:owner-chemistry.:.ccl.net>> wrote: > > James what you are asking is impossible to answer as it depends on > a number of parameters like the type of computer you use, the size > of your system and the level of accuracy (theory and/or basis set) > you want your results to have. > > Traditionally for the same system and basis set HF is faster than > DFT and DFT is faster than CCSD (the later one coincidentally is > an expensive method) > > I am sorry I cannot provide a more comprehensive answer but in > reality you are constrained by the parameters I have outlined above. > > Regardless I hope this helps > > Thomas > > Thomas Gkourmpis > Researcher- Innovation & Technology > > Borealis AB | SE-444 86 Stenungsund | Sweden > Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 > www.borealisgroup.com <http://www.borealisgroup.com/>| 556078-6633 > | Swedish Companies Registration Office > > thomas.gkourmpis]-[borealisgroup.com > <mailto:thomas.gkourmpis]-[borealisgroup.com> > > ___________________________________ > Borealis - Shaping the Future with Plastics > > *From:*owner-chemistry+thomas.gkourmpis==borealisgroup.com > <http://borealisgroup.com>]-[ccl.net <http://ccl.net> > [mailto:owner-chemistry+thomas.gkourmpis > <mailto:owner-chemistry%2Bthomas.gkourmpis>==borealisgroup.com > <http://borealisgroup.com>]-[ccl.net <http://ccl.net>] *On Behalf > Of *J D Whitfield jdwhitfield * gmail.com <http://gmail.com> > *Sent:* Monday, January 28, 2013 8:30 PM > *To:* Gkourmpis, Thomas > *Subject:* CCL:G: Facing difficulty in running g03 peogramm > > What method are you using (e.g. HF, DFT, CCSD, etc)? This can > make a big difference in the run-time. Also what qualifies as a > "very long time"? > > James > > > -- > > > Dr. J. D. Whitfield > > VCQ Postdoctoral Fellow > > Vienna Center for Quantum Science and Technology > > email: james.whitfield() univie.ac.at > <mailto:james.whitfield%28%29%20univie.ac.at> > > web: homepage.univie.ac.at/james.whitfield > <http://homepage.univie.ac.at/james.whitfield> > > On Mon, Jan 28, 2013 at 12:03 PM, Manjunath Ningappa Wari > sm5wari^^^gmail.com <http://gmail.com> <owner-chemistry() ccl.net > <mailto:owner-chemistry%28%29%20ccl.net>> wrote: > > > Sent to CCL by: "Manjunath Ningappa Wari" [sm5wari^^gmail.com > <http://gmail.com>] > I am calculating dipole moment in ground state for coumarine > molecules using > g03 program. It is taking very long time to calculate, so plz > suggest me how to > run faster the g03 program. > > Thanking you > Manjunath Wari > Dept of Physics > Karnatk University > Dharwad. > > e-mail: sm5wari_._gmail.com <http://gmail.com> > > > > -= This is automatically added to each message by the mailing > script =-<br > > > E-mail to subscribers: CHEMISTRY() ccl.net > <mailto:CHEMISTRY%28%29%20ccl.net> or use:> > E-mail to administrators: CHEMISTRY-REQUEST() ccl.net > <mailto:CHEMISTRY-REQUEST%28%29%20ccl.net> or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> <br> > This Email and any files transmitted with it are confidential and > intended solely for the use of the individual or the entity to > whom it is addressed. If you have received this Email by error, > please notify the sender and delete the material from any storage > device. Borealis extends no warranties and makes no > representations as to the accuracy or completeness of the > information provided. It is the customer's responsibility to > inspect and test our products and technical advice in order to > satisfy itself as to the suitability of the products and technical > advice for the customer's particular purpose. > > From owner-chemistry@ccl.net Wed Jan 30 20:25:00 2013 From: "Sina Behtash behtash!=!email.sc.edu" <owner-chemistry|a|server.ccl.net> To: CCL Subject: CCL: COSMO vs COSMO-RS Message-Id: <-48158-130130181352-30265-61ExEcgEI6Yy2M6+alOZKA|a|server.ccl.net> X-Original-From: "Sina Behtash" <behtash%email.sc.edu> Date: Wed, 30 Jan 2013 18:13:51 -0500 Sent to CCL by: "Sina Behtash" [behtash ~ email.sc.edu] I am using both COSMO (implemented in Turbomole 6.0) and COSMOtherm/COSMO-RS to calculate the solvent effects on the free energy of reaction for the following reaction: Glucose --> HMF + 3 H2O First, I optimized all the reactants and products in the gas phase using b3-lyp and a def2-QZVP basis set. Next, assuming that the geometry does not change significantly in the presence of water, I used the optimized structure to run a COSMO single-point energy calculation with the same basis set and dielectric constant of water at 298 K which is 78.39. According to the COSMO calculation, GReaction-COSMO - GReaction-gas= -15.2 Kcal/mol Next, in order to generate relevant input for COSMO-RS calculations, I ran another COSMO single-point energy calculation using the BP functional and TZVP basis set. Then I used COSMOtherm/Reactions and the BP-TZVP data base to run COSMO-RS calculations for my reaction at T=298K. The result shows that, GReaction-COSMO-RS-Water - GReaction-gas= -2.05 Kcal/mol I was expecting that for water, the COSMO and COSMO-RS calculations should give almost the same result. However, in this case the difference in the effect of water on the free energy of reaction is around 13 Kcal/mol. Can anyone explain to me why the difference is so large? Im wondering if the effects of hydrogen bonding and electrostatic interactions can be this significant. Sina Behtash Ph.D. Student Department of Chemical Engineering University of South Carolina Phone: (803)777-0611 Email: behtash!=!email.sc.edu From owner-chemistry@ccl.net Wed Jan 30 23:56:00 2013 From: "Elaine Meng meng,,cgl.ucsf.edu" <owner-chemistry%%server.ccl.net> To: CCL Subject: CCL: new release of UCSF Chimera Message-Id: <-48159-130130194220-1526-RQ7WBPRc6fE7bpeHpC516g%%server.ccl.net> X-Original-From: "Elaine Meng" <meng!A!cgl.ucsf.edu> Date: Wed, 30 Jan 2013 19:42:19 -0500 Sent to CCL by: "Elaine Meng" [meng_-_cgl.ucsf.edu] Hello everybody, A new production release of UCSF Chimera (version 1.7) is available: http://www.cgl.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). Note: 1.6 was the last version to support Mac PPC and OS X 10.5. New features include faster loading and graphics, improvements in lighting and interactive shadows, "click-to-center" mouse mode, map display as orthogonal planes, interface to Modeller for building missing loops, Animation timeline, enhanced commands for animation, interfaces to PDB2PQR, APBS, and AutoDock Vina single-ligand docking. More details are given below; see release notes for the full list: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.7.html Graphics, Depiction: * faster loading of large molecules * faster graphics on many systems; target frame rate raised to 60 fps * interactive shadows: finer quality; available on more systems * glossy default lighting, better control over contrast * users can create custom presets * 2D Labels can have backgrounds (colored rectangles beneath) * PipesAndPlanks can color SSEs uniquely, show arrowheads * Actions...Color menu works on axis, plane, and centroid objects * CASTp pocket display omits small surface fragments * "surface" and "sop" command options to hide small fragments Animation: * Animation tool allows placing scenes and simple actions (rock, roll) along a timeline to define a movie * new output movie formats H.264, VP8/WebM, Theora * "play" command to animate complex motions like radial explosion * "transparency" command to set transparency of atoms, ribbons, etc. without otherwise changing their colors, can be applied gradually * "movie" command usability improvements * "perframe" allows embedding other commands directly, substituting variables other than frame count, executing at multiframe intervals * "roll" and "turn" command options for precession motion Structure Analysis and Modeling: * AmberTools updated to v12, default charges etc. now Amber ff12SB * "click-to-center" mouse mode (default Ctrl-right button) * "show distances to nearby residues" added to atom context menu * interface to Modeller for building missing segments * interface to APBS Poisson-Boltzmann electrostatics calculations * interface to PDB2PQR charge and radius assignment * interface to AutoDock Vina single-ligand docking * ViewDock support for AutoDock/Vina .pdbqt, GOLD .mol2 files * MD Movie can calculate average structures, plot RMSD vs. frame, read GROMACS .xtc format; occupancy calculation can treat atoms as VDW spheres (as opposed to points only) * Build Structure bond length slider, bond angle control * Multalign Viewer can use a subset of the existing sequences (rather than all) to guide alignment of a new sequence; the Region Browser lists individual-sequence regions separately (now that a sequence can have many UniProt annotations) Density Maps: * Volume Viewer orthogonal planes feature * Volume Tracer default mode includes placing markers on planes * "fitmap" option to fit multiple models independently * "vop cover" can extend a map using its symmetries Enjoy! On behalf of the Chimera team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco