From owner-chemistry@ccl.net Thu Feb 11 00:54:00 2010 From: "David Gallagher gallagher.da .. gmail.com" To: CCL Subject: CCL: Turbomole Training Course, March 2010 Message-Id: <-41239-100211005055-16908-adt7VlczUyYyJAHbkK4vKw-#-server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_14836750==.ALT" Date: Wed, 10 Feb 2010 20:48:03 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da[*]gmail.com] --=====================_14836750==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Turbomole (quantum chemistry) Training Course, 23rd March 2010 An introductory training course for Turbomole will be held during the ACS meeting in San Francisco on Tuesday 23rd March 2010 (late afternoon). New users and anyone interested to learn more about Turbomole are welcome to register to for this free training session (about 1 hour). A copy of Turbomole will be provided, but please bring your own laptop. Further information will be posted at http://cacheresearch.com/aiche.html#training when available. David Gallagher CAChe Reseach --=====================_14836750==.ALT Content-Type: text/html; charset="us-ascii" Turbomole (quantum chemistry) Training Course, 23rd March 2010

An introductory training course for Turbomole will be held during the ACS meeting in San Francisco on Tuesday 23rd March 2010 (late afternoon).  New users and anyone interested to learn more about Turbomole are welcome to register to <dgallagher(AT)CACheResearch.com> for this free training session (about 1 hour).  A copy of Turbomole will be provided, but please bring your own laptop.  Further information will be posted at http://cacheresearch.com/aiche.html#training when available.

David Gallagher
CAChe Reseach --=====================_14836750==.ALT-- From owner-chemistry@ccl.net Thu Feb 11 04:41:01 2010 From: "Manish Agarwal zmanish/./gmail.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41240-100211041652-23996-Y4sdxCil1+cgq6e7NzKvqw]|[server.ccl.net> X-Original-From: Manish Agarwal Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 11 Feb 2010 13:38:39 +0530 MIME-Version: 1.0 Sent to CCL by: Manish Agarwal [zmanish]~[gmail.com] My sincere apologies for the delayed update. Many thanks to all the responses I have got. This is a long mail, and is purely an update - so I am still running simulations. A small recounting of events: NPT Molecular dynamics Simulation of TIP5P water model, Cubic Boundary Conditions, Ewald Summation for Electrostatics, Quaternion for rigid body motion, Timestep 0.001ps (1fs) Target Temperature 300K, pressure 1atm (0.001 katm) 256 water molecules: 1 million steps Berendesen Themostat (20ps) and barostat(1ps) Pressure 9.1328E-04 katm Temperature 2.7879E+02 Volume: 7.7622E+03 Density:0.985 256 water molecules: 2 million steps Berendesen Themostat (0.1ps) and barostat(0.5ps) Pressure 4.2339E-03 katm Temperature 2.9982E+02 Volume : 7.7838E+03 Density: 0.983 >>>>>Here is what I did, following excellent discussion here, 500 Molecules of water (tip5p) 1million steps (1ns) Berendesen Themostat (2ps) and barostat(0.5ps) Pressure 1.1679E-03 katm Temperature 2.9812E+02 Volume : 1.5194E+04 Density: 0.983 1000 Molecules of water (tip5p) 1million steps (1ns) Berendesen Themostat (2ps) and barostat(0.5ps) Pressure 1.1679E-03 katm Temperature 2.9812E+02 Volume : 3.0412E+04 Density: 0.982 I am starting up longer runs 4-6ns- and currently I have 40h/ns for 1000 molecules and 24h/ns for 500 molecules Regards Manish Agarwal Senior Research Scholar Department of Chemistry Indian Institute of Technology, Delhi - - - - - - - - - - - - - - - - - - - - - - - - - - - On 7 February 2010 17:26, Manish Agarwal zmanish#,#gmail.com wrote: > > Sent to CCL by: Manish Agarwal [zmanish|*|gmail.com] > Dear CCLers > > Excellent suggestions, that too on the weekend ... My thanks to all. > I should have mentioned =A0that I am using cubic Periodic Boundary. > > Here is what I intend to do: > > The time step of 1 fs is, in my opinion, not too low or too high for > bulk water simulations at temperatures where there are no slow > dynamics. > > I _am_ going to increase the number of molecules, and see if it > changes the outcome - 500, and 1000. > I am also going to increase the number of simulation timesteps - 4-6 > million should suffice for the test. I will also try Nose-Hoover > thermostat-barostat combination. > > In the past I have run Berendsen NVT simulations with tau=3D200ps with > no problems - although, reviewers have complained it to be 'too high'. > The large relaxation time allows for internal dynamics to be as near > NVE as possible, specially near temperatures below the model's melting > point. But this is my first brush with NPT. > > My main concern has been that I am trying to compare MD-NPT results > with those obtained from MC-NPT. > > I will try and post my results in the next 24-48 hours... > > Looking forward to more discussion, > Regards, and thanks again. > Manish Agarwal > - - - - - - - - - - - - - - - - - - - - - - - - - - - > > > On 6 February 2010 23:02, Venable, Richard (NIH/NHLBI) E > venabler!A!nhlbi.nih.gov wrote: >> >> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-*-nhlbi.nih= .gov] >> I have to disagree. >> >> If there are suspected stability problems, the last thing one should do = is to increase the timestep. >> >> The weak coupling scheme typified by the Berendsen thermostat and barost= at have been justly criticized by many, including Allen and Tildesley; Nose= -Hoover extended system approaches are regarded as considerably less flawed= . >> >> Starting from 0 K is usually not necessary, and can be ill advised in so= me programs. =A0Anything below 200 K should be just fine. >> >> I don't believe one can run NPT without periodic boundaries. >> >> -- >> Rick Venable >> compuational chemist >> >> ________________________________________ >>> From: owner-chemistry+rick_venable=3D=3Dnih.gov||ccl.net [owner-chemist= ry+rick_venable=3D=3Dnih.gov||ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m= .ibrahim[a]compchem.net [owner-chemistry||ccl.net] >> Sent: Saturday, February 06, 2010 11:17 AM >> To: Venable, Richard (NIH/NHLBI) [E] >> Subject: CCL: NPT TIP5P, 1atm MD >> >> Dear Manish >> I am not familiar with DL Ploy. >> But, if you don't mind, you can have a go with the following issues to r= eproduce the water density: >> * Use NPT ensemble with relaxation time of 2.0ps >> * Use Berendsen Thermostat with 0.5ps time constant >> * Use Periodic Boundary Condition (Important) >> * If it is available, start your run from 0K and increase the temperatur= e gradually until reaches 300K. (During heating step, use constant volume b= oundary condition). >> >> Have a go with these issues, Good look >> Sincerely; >> M. Ibrahim >> >> >> On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com > = wrote: >> >> Sent to CCL by: Manish Agarwal [zmanish^^gmail.com] >> Dear CCLers, >> >> I am having trouble reproducing the density at 1 atm, 300K for TIP5P >> water, or for that matter any water model in the NPT ensemble using >> Molecular Dynamics: >> >> have tried >> Berendsen Thermostat and Barostat >> Nose-Hoover Thermostat and Barostat >> >> am using Ewald summation for electrostatics, >> 256 water molecules. 2000000 =A0steps, with or without velocity scaling >> in the beginning 1fs time step >> DLPOLY ver 2.19 >> >> The problem is as follows : either the pressure does not stabilize at >> 1atm (too low or too high) or the temperature does not maintain at >> 300K >> When both are maintained, for example Berendsen Thermostat relaxation >> time 0.1ps, Barostat relaxation time 0.5ps, the density does not reach >> 0.99g/cc; also, the energy profile with time looks too perturbed (does >> NOT look like a nice fluctuation about the mean). >> >> In the NVT ensemble, however, I have been able to reproduce other >> static(orientational order) and dynamic properties(diffusivities) - so >> the model seems fine. >> >> Any thoughts, suggestions are appreciated. >> >> Regards, >> Manish Agarwal >> > >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY{=3Dcl.net o= r use:E-mail to administrators: CHEMISTRY-REQUEST{=3Dcl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp= ://www.ccl.net/spammers.txt >> >> >> - This is automatically added to each message by the mailing script -> = =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/= chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> >> >> > > > > - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Feb 11 05:47:01 2010 From: "Manoj Rudraraju manojrudraraju=-=gmail.com" To: CCL Subject: CCL: Articles on Covalently bound ligands (covalently docked) Message-Id: <-41241-100211054507-21668-iqgVrjHLQolQb+nYzlVZIg%%server.ccl.net> X-Original-From: "Manoj Rudraraju" Date: Thu, 11 Feb 2010 05:45:03 -0500 Sent to CCL by: "Manoj Rudraraju" [manojrudraraju!^!gmail.com] Dear All, I am looking for Review articles or research articles related to Covalently bound ligands (experimental or/and theoritical), Covalent docking (theoritical papers) I am in the process of writing up small research paper with few results in hand and it would be great scientific help if anyone can provide me titles or articles Thanks in Advance. regards Manoj From owner-chemistry@ccl.net Thu Feb 11 09:19:01 2010 From: "Carsten Detering detering^^^biosolveit.de" To: CCL Subject: CCL: BioSolveIT Workshop on FBLD and SBLD - Early registration ends soon! Message-Id: <-41242-100211032125-15984-GGW96qzPR/3pLcnlTOwrMg:server.ccl.net> X-Original-From: "Carsten Detering" Date: Thu, 11 Feb 2010 03:21:21 -0500 Sent to CCL by: "Carsten Detering" [detering-,-biosolveit.de] Dear CClers, BioSolveIT is proud to announce a free-of-charge workshop on FBLD and SBLD, in which our novel team-building software platform for fragment and structure-based drug design - LeadIT will have its world premiere. Who should attend: Medicinal and Computational Chemists Where: San Francisco, CA, close to the ACS-Meeting site (tba) When: Sunday, March 21, 2010, 4pm. Prof. Hugo Kubinyi, a world renown Medicinal Chemist with 40+ years of experience in drug discovery will kick off the workshop with a seminar: Scaffold Hops - Fact or Fiction? During the workshop you will learn LeadIT's capabilities to * form teams of CompChems and MedChems * grow fragments * link and merge fragments * replace unwanted substructures * confirm generated structures via docking. **HURRY UP! The deadline for early registration ends Valentine's day, Feb 14, 2010** There are many good reasons to register early: 1. From the time of your registration up until the workshop and 3 months beyond you may evaluate LeadIT free of charge. 2. Attendees who have registered BEFORE Valentine's Day (Feb 14th, 2010) will participate in a laptop raffle. 3. Space at the workshop is limited and seats are expected to sell out early. For more information (and to register), visit our web page: www.biosolveit.com/workshops/2010/01 Be the first to experience the team-building software number 1 for Computational and Medicinal Chemists L-e-a-d-I-T. We are looking forward to seeing you in SF! __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering=biosolveit.com Phone EU: +49-2241-2525-0 / Fax: -525 www.biosolveit.com Phone US: +1-617-297-2770 BioSolveIT GmbH - An der Ziegelei 79 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 From owner-chemistry@ccl.net Thu Feb 11 10:45:01 2010 From: "Mohamed naseer Ali mmdnaseer,,gmail.com" To: CCL Subject: CCL:G: Restarting NMR calculations Message-Id: <-41243-100211104252-21156-dd/qhvoo6wlJ+yQz5t5gKw]-[server.ccl.net> X-Original-From: "Mohamed naseer Ali" Date: Thu, 11 Feb 2010 10:42:48 -0500 Sent to CCL by: "Mohamed naseer Ali" [mmdnaseer:gmail.com] All: My gaussian03 NMR calculation got crashed due to wall time limit. Is there any way of restarting this terminated NMR calculations. Suggestions and comments would be appreciated. Thanks From owner-chemistry@ccl.net Thu Feb 11 11:35:00 2010 From: "Jonathan Stevens stevenje/a\udmercy.edu" To: CCL Subject: CCL: splitting basis functions Message-Id: <-41244-100211111800-7481-RsVihsAoQWP0KiDzr5NuEw(~)server.ccl.net> X-Original-From: Jonathan Stevens Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 11 Feb 2010 15:44:14 GMT MIME-Version: 1.0 Sent to CCL by: Jonathan Stevens [stevenje() udmercy.edu] I have done some reading on defining sets of two or three basis function from 1 by "splitting"; for example, a fucntion with exponent a can be "split" into two by defining new exponents 2*a and a/2 to make a "tight" and "diffuse" pair. In particular, I would like to try splitting "f" polarization functions- does anyone know of a good reference for a guide, or instructions, or information on this? Thanks. Jonathan E. Stevens Department of Chemistry and Biochemistry University of Detroit Mercy 4001 W. McNichols Road Detroit, MI 48221 stevenje.:.udmercy.edu 313-993-1048