From owner-chemistry@ccl.net Thu May 18 05:43:00 2006 From: "Marcel Drabbels Marcel.Drabbels-*-epfl.ch" To: CCL Subject: CCL:G: Running Two jobs on a shared memory computer Message-Id: <-31773-060518052851-30189-bp19kU4CXFImbhAxlK1Mmw*|*server.ccl.net> X-Original-From: Marcel Drabbels Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Thu, 18 May 2006 10:28:41 +0200 Mime-Version: 1.0 Sent to CCL by: Marcel Drabbels [Marcel.Drabbels###epfl.ch] Dear Roger, This sounds very much like the problem we recently encountered with Gaussian when we tried to run it on our dual opteron system running SUSE 9.3. Most of the time jobs making use of two processors crashed. The people at Gaussian suggested that this might be caused by a bug in the older LINUX kernels that caused a race condition. We recently updated our kernel to version 2.6.16. And indeed the problems have disappeared. Marcel, At 17-05-06 13:09, you wrote: >Sent to CCL by: Roger Kevin Robinson [r.robinson|,|imperial.ac.uk] >Hi, > > I have several shared processor opterons. At the moment I can not >run guassian on two shared memory processors with out it crashing. > >If I try to run two jobs separately the both end up running on the same >processor. > >Is there any way to get both jobs to run on separate processors. > >Thanks Roger==================================================================== Dr. Marcel Drabbels Laboratoire de Chimie Physique Moléculaire (LCPM) École Polytechnique Fédérale de Lausanne (EPFL) Station 6 CH-1015 Lausanne Switzerland Tel: +41-21-693 3022/6131 Fax: +41-21-693 5170 http://lcpm.epfl.ch/ ==================================================================== From owner-chemistry@ccl.net Thu May 18 07:57:00 2006 From: "Nathan Scott scottjn_+_gmail.com" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31774-060517104442-10910-T6e7N3FE/I0xmQSJ/bwuvg!^!server.ccl.net> X-Original-From: "Nathan Scott" Content-Type: multipart/alternative; boundary="----=_Part_73405_27921155.1147873290092" Date: Wed, 17 May 2006 09:41:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Nathan Scott" [scottjn(!)gmail.com] ------=_Part_73405_27921155.1147873290092 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Greetings CCLers. Can anyone point me to a reference discussing the computational cost of QM/MM simulations and how it scales with size of the components? I have some experience with quantum chemistry simulations, as well as molecular dynamics simulations, but I'm new to QM/MM and am being asked as part of a proposal I'm writing to discuss the computational cost o= f the calculations I want to do. Right now the plan is to solvate a simple 6 atom quantum mechanical system with approximately 1000 TIP4P water molecules. Thanks in advance for any help you can provide. J. Nathan Scott Graduate Student University of Pennsylvania Biochemistry and Molecular Biophysics Graduate Group Work Phone: +1.215.898.8783 ------=_Part_73405_27921155.1147873290092 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Greetings CCLers.  Can anyone point me to a reference discussing the c= omputational cost of QM/MM simulations and how it scales with size of the c= omponents?  I have some experience with quantum chemistry simulations,= as well as molecular dynamics simulations, but I'm new to QM/MM and am bei= ng asked as part of a proposal I'm writing to discuss the computational cos= t of the calculations I want to do.  Right now the plan is to solvate = a simple 6 atom quantum mechanical system with approximately 1000 TIP4P wat= er molecules.


Thanks in advance for any help you can provide.

J. Natha= n Scott
Graduate Student
University of Pennsylvania
Biochemistry a= nd Molecular Biophysics Graduate Group
Work Phone: +1.215.898.8783
------=_Part_73405_27921155.1147873290092-- From owner-chemistry@ccl.net Thu May 18 09:00:01 2006 From: "Shobe, David dshobe(!)sud-chemieinc.com" To: CCL Subject: CCL:G: 3rd-row G3 G3MP2 and G3B3 under G03W? Message-Id: <-31775-060518085907-3963-o/3LJNpzR+8/BpbyMYDK7A-,-server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 18 May 2006 14:58:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe]-[sud-chemieinc.com] I thought the list might like to know: Gaussian Inc. has assured me that the G3 method and variants use the correct 6-31G* basis set for third-row elements, so there's no need to worry about getting an incorrect answer. However, I tried a G3B3 calculation on Br atom and it crashed due to lack of a GTLarge basis set for that atom. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] Sent: Wednesday, May 17, 2006 9:46 AM To: Shobe, David Subject: CCL:G: 3rd-row G3 G3MP2 and G3B3 under G03W? Sent to CCL by: "Shobe, David" [dshobe(!)sud-chemieinc.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C679B6.44ED5C8C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Can one expect correct answers when calculating G3, G3MP2 or G3B3 energies = using Gaussian 03W for a species containing 3rd-row main group elements (K-= Ca, Ga-Br)? I ask because certain established basis sets (includng 6-31G*) were redefin= ed for the purposes of G3 calculations when the method was extended to 3rd-= row elements.=20 --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, you should not use, copy, disclose or take any action based on this e-= mail or any information contained in the message. If you have received this= material in error, please advise the sender immediately by reply e-mail an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C679B6.44ED5C8C Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable 3rd-row G3 G3MP2 and G3B3 under G03W?

Can one expect correct answers when calcul= ating G3, G3MP2 or G3B3 energies using Gaussian 03W for a species containin= g 3rd-row main group elements (K-Ca, Ga-Br)?

I ask because certain established basis se= ts (includng 6-31G*) were redefined for the purposes of G3 calculations whe= n the method was extended to 3rd-row elements.

--David Shobe, Ph.D., M.L.S.
S=FCd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a fire= wall.




This e-mail message may contain confidential and / or privileged infor= mation. If you are not an addressee or otherwise authorized to receive this= message, you should not use, copy, disclose or take any action based on th= is e-mail or any information contained in the message. If you have received= this material in error, please advise the sender immediately by reply e-ma= il and delete this message.
Thank you.
------_=_NextPart_001_01C679B6.44ED5C8C--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Thu May 18 10:02:00 2006 From: "Joseph T Golab joseph.golab{}innovene.com" To: CCL Subject: CCL: FOMMS 2006 Early Registration Extension until June 1 2006 Message-Id: <-31776-060518094611-32683-VhHFY1DZjbVXN/y0zzwM2A(-)server.ccl.net> X-Original-From: "Joseph T Golab" Date: Thu, 18 May 2006 09:46:06 -0400 Sent to CCL by: "Joseph T Golab" [joseph.golab!=!innovene.com] Because of a change in publisher of the CD-ROM and abstract book, we take this opportunity to announce that the deadline for FOMMS 2006 Early Registration is now June 1! 3rd International Conference on the Foundations of Molecular Modeling and Simulation (FOMMS 2006), Semiahmoo Resort, Blaine, WA, USA, July 9th - 14th, 2006 >> Deadline for Early Registration June 1 2006 << The 3rd International Conference on the Foundations of Molecular Modeling and Simulation (FOMMS), will be held July 9th - 14th, 2006, at Semiahmoo Resort (www.semiahmoo.com), in Blaine, WA, USA. Easily accessible from Seattle WA or Vancouver BC, FOMMS 2006 is a scientific meeting balanced between the methods of quantum mechanics, atomistic simulation, mesoscale methods and beyond, with application areas in chemistry, biology, and materials. FOMMS is the only focused conference that brings together such a broad modeling community and emphasizes integration from atomistic to meso- & macro-scale modeling. A detailed conference agenda as well as housing and travel information are available at the FOMMS 2006 website (www.fomms.org). Since we are rapidly approaching our maximum attendance target, you are encouraged to take advantage of early registration as soon as possible. FOMMS 2006 Program Keynote Address Professor Mark A. Ratner Nanoscience & Nanotechnology Professor Glenn Fredrickson Professor Katsumi Kaneko Professor Jerzy Bernholc Contributed Poster Session A Education Dr. Warren Hehre Professor Michael Allen Polymeric Materials Professor Kurt Kremer Dr. Shi-aki Hyodo Professor Mark W. Matsen Advances in Modeling & Simulation Dr. Philippe Ungerer Professor Denis Evans Biological Applications Professor Carol K. Hall Professor Shekhar Garde Professor Gerhard Hummer Methods & Applications for Materials Modeling Professor Gregory A. Voth Professor C. Richard A. Catlow Reaction Engineering Professor Emily A. Carter Professor Randall Q. Snurr Professor Rutger A. van Santen Contributed Poster Session B Future Vision Professor Vijay Pande Dr. Patricia T. Sparrell Dr. Thom Dunning For additional information about the conference please visit our web site or contact us directly at chair^^fomms.org. Joe Golab (Ineos Technoloiges) & Clare McCabe (Vanderbilt University) FOMMS 2006 Conference Chairs, chair^^fomms.org From owner-chemistry@ccl.net Thu May 18 10:36:01 2006 From: "neeraj misra misraneeraj^gmail.com" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31777-060518100124-5363-ZEtApOORuJwEnBkHTw+nog**server.ccl.net> X-Original-From: "neeraj misra" Content-Type: multipart/alternative; boundary="----=_Part_3117_12196256.1147960879086" Date: Thu, 18 May 2006 19:31:19 +0530 MIME-Version: 1.0 Sent to CCL by: "neeraj misra" [misraneeraj|*|gmail.com] ------=_Part_3117_12196256.1147960879086 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Nathan, I am writing a paper on MM/QM calculations on a biomolecule.I can tell you it involves hell of a time. On 5/18/06, Nathan Scott scottjn_+_gmail.com wrote: > > Sent to CCL by: "Nathan Scott" [scottjn(!)gmail.com] > > ------=_Part_73405_27921155.1147873290092 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > Greetings CCLers. Can anyone point me to a reference discussing the > computational cost of QM/MM simulations and how it scales with size of the > components? I have some experience with quantum chemistry simulations, as > well as molecular dynamics simulations, but I'm new to QM/MM and am being > asked as part of a proposal I'm writing to discuss the computational cost > o= > f > the calculations I want to do. Right now the plan is to solvate a simple > 6 > atom quantum mechanical system with approximately 1000 TIP4P water > molecules. > > > Thanks in advance for any help you can provide. > > J. Nathan Scott > Graduate Student > University of Pennsylvania > Biochemistry and Molecular Biophysics Graduate Group > Work Phone: +1.215.898.8783 > > ------=_Part_73405_27921155.1147873290092 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > Content-Disposition: inline > > Greetings CCLers.  Can anyone point me to a reference discussing the > c= > omputational cost of QM/MM simulations and how it scales with size of the > c= > omponents?  I have some experience with quantum chemistry > simulations,= > as well as molecular dynamics simulations, but I'm new to QM/MM and am > bei= > ng asked as part of a proposal I'm writing to discuss the computational > cos= > t of the calculations I want to do.  Right now the plan is to solvate > = > a simple 6 atom quantum mechanical system with approximately 1000 TIP4P > wat= > er molecules. >


Thanks in advance for any help you can provide.

J. > Natha= > n Scott
Graduate Student
University of Pennsylvania
Biochemistry > a= > nd Molecular Biophysics Graduate Group
Work Phone: +1.215.898.8783
> > ------=_Part_73405_27921155.1147873290092--> > > > -- Neeraj Misra PhD Assoc.Prof in Physics Lucknow University 226007 Phone 0522-2740410 (O) 0522-3253647 (R) ------=_Part_3117_12196256.1147960879086 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Nathan,
                 I am writing a paper on MM/QM calculations on a biomolecule.I can tell you it involves hell of a time.

 
On 5/18/06, Nathan Scott scottjn_+_gmail.com <owner-chemistry-,-ccl.net> wrote:
Sent to CCL by: "Nathan Scott" [scottjn(!)gmail.com]

------=_Part_73405_27921155.1147873290092
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

Greetings CCLers.  Can anyone point me to a reference discussing the
computational cost of QM/MM simulations and how it scales with size of the
components?  I have some experience with quantum chemistry simulations, as
well as molecular dynamics simulations, but I'm new to QM/MM and am being
asked as part of a proposal I'm writing to discuss the computational cost o=
f
the calculations I want to do.  Right now the plan is to solvate a simple 6
atom quantum mechanical system with approximately 1000 TIP4P water
molecules.


Thanks in advance for any help you can provide.

J. Nathan Scott
Graduate Student
University of Pennsylvania
Biochemistry and Molecular Biophysics Graduate Group
Work Phone: +1.215.898.8783

------=_Part_73405_27921155.1147873290092
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

Greetings CCLers.&nbsp; Can anyone point me to a reference discussing the c=
omputational cost of QM/MM simulations and how it scales with size of the c=
omponents?&nbsp; I have some experience with quantum chemistry simulations,=
as well as molecular dynamics simulations, but I'm new to QM/MM and am bei=
ng asked as part of a proposal I'm writing to discuss the computational cos=
t of the calculations I want to do.&nbsp; Right now the plan is to solvate =
a simple 6 atom quantum mechanical system with approximately 1000 TIP4P wat=
er molecules.
<br><br><br>Thanks in advance for any help you can provide.<br><br>J. Natha=
n Scott<br>Graduate Student<br>University of Pennsylvania<br>Biochemistry a=
nd Molecular Biophysics Graduate Group<br>Work Phone: +1.215.898.8783<br>

------=_Part_73405_27921155.1147873290092--



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--
Neeraj Misra PhD
Assoc.Prof in Physics
Lucknow University 226007
Phone 0522-2740410 (O)
           0522-3253647 (R) ------=_Part_3117_12196256.1147960879086-- From owner-chemistry@ccl.net Thu May 18 12:12:00 2006 From: "Mgr. Lubos Vrbka lubos.vrbka : uochb.cas.cz" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31778-060518121042-11469-cKmcLDjeBa4+HagYXhcEfA!=!server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2 Date: Thu, 18 May 2006 18:10:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka[a]uochb.cas.cz] dear nathan, > Greetings CCLers. Can anyone point me to a reference discussing the > computational cost of QM/MM simulations and how it scales with size of the > components? I have some experience with quantum chemistry simulations, as > well as molecular dynamics simulations, but I'm new to QM/MM and am being > asked as part of a proposal I'm writing to discuss the computational cost o= > f > the calculations I want to do. Right now the plan is to solvate a simple 6 > atom quantum mechanical system with approximately 1000 TIP4P water > molecules. i don't have any reference, but it's not that big problem to estimate the result. the computational cost of the MD algorithm per 4000 atom and one timestep will be in any case much shorter then the cost of any decent QM method. only if you use some really cheap semiempirical method as QM and very large number of atoms in the MM region (but certainly more than 4000), it *might* become comparable. btw, for 1000 water molecules, you can expect to get several nanoseconds per day from MD simulation. i don't know what QM method you need to use. of course you'll use wavefunction from the previous step as a guess for the current step, but still... if you do QM/MM optimization then depending on the setup and system (very large total number of atoms, small QM region, cheap QM), the diagonalization of the hessian might be the most time demanding step, but it doesn't seem to be your case. to conclude, you can almost certainly expect that the QM calculation will be the time determining step. regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic http://www.molecular.cz/~vrbka ..................................................... From owner-chemistry@ccl.net Thu May 18 13:21:00 2006 From: "Ross Walker ross]|[rosswalker.co.uk" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31779-060518130944-6256-Dz/DSR6zbs1p1wuH+j+Abw],[server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 May 2006 10:09:33 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk] Hi Nathan, > Greetings CCLers. Can anyone point me to a reference discussing the > computational cost of QM/MM simulations and how it scales > with size of the > components? I have some experience with quantum chemistry > simulations, as > well as molecular dynamics simulations, but I'm new to QM/MM > and am being > asked as part of a proposal I'm writing to discuss the > computational cost o= > f > the calculations I want to do. Right now the plan is to > solvate a simple 6 > atom quantum mechanical system with approximately 1000 TIP4P water > molecules. This really depends on the type of QM calculation you plan on doing which you don't state. Semi-empirical is significantly cheaper than full ab initio. For what you suggest above if you wanted to do semi-empirical you can use Amber 9 and the computational cost will be about 6% more than doing the calculation classically. You can probably go to about 90 QM atoms or so before it even starts to become expensive. Plus you can do a simulation with a full treatment of electrostatics and periodic boundaries for both the QM and MM regions using PME. Without a PME treatment you will need to use an infinite (i.e. no) cutoff and probably add an implicit solvent treatment for the gas phase region of your system to get meaningful results. Using a cut off with gas phase / water cap simulations introduces serious artefacts into your simulation and can completely invalidate your results. Hence often it can be quicker to do a full PME treatment than to run the gas phase non-periodic simulation. A lot of work has been put into making Amber 9's QM support as fast as possible while preserving accuracy in the gradients. It is around 10 times quicker than Amber 8 and Charmm c32. The Amber 9 QMMM implementation is currently being added to Charmm and will I believe be released shortly. As a quick guide here are the timings I got for two water molecules treated with PM3 and then solvated with a rectangular box consisting of 332 TIP4P water molecules. PME was run with an 8 angstrom MM and QM direct space cut off, shake was used for both the MM and QM region, langevin thermostating was used at 300K and a timestep of 2fs was used. For the gas phase simulation I used an infinite MM and QM cut off. The default SCF convergence of 1.0x10-8 KCal/mol was used. This is for a pentium-D 3.4GHz 2MB L2 cache machine. Time is for 2000 steps = 4ps. 1 cpu 2 cpu's time(s) ns/day time(s) ns/day PME classical = 39.99 8.64 23.35 14.80 PME QMMM = 62.15 5.56 40.15 8.83 Gas phase clas= 123.67 2.79 64.48 5.36 Gas phase QMMM= 130.99 2.64 70.12 4.93 So for the system you want to study it really won't cost you much at all. However, if you want to do a full abinitio treatment then it could get very expensive. All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross[]rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Thu May 18 13:56:00 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas!=!urv.cat" To: CCL Subject: CCL: AutoDock's parameters for cooper? Message-Id: <-31780-060518134519-25598-Oa3FgK2BgJramveFTF6Efw=-=server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Thu, 18 May 2006 19:44:51 +0200 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas-.-urv.cat] Dear CCL list members, we would like to dock some ligands into a receptor that has cooper has a cofactor. Then, I wonder if any of you have the Rij and epsij parameters for Cu-Cu that are suitable for their use with AutoDock v3.05 With many thanks in advances for your help Gerard -- ============================= NOTE: NEW E-MAIL ============================ Dr. Gerard Pujadas Grup de recerca en Nutrigenòmica Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas^^urv.cat Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Thu May 18 14:31:00 2006 From: "jim pfaendtner pfaendtner++northwestern.edu" To: CCL Subject: CCL: TheRate kinetics code Message-Id: <-31781-060518141051-16479-bWv3Ckcc3LoqR42qKS0ARA=server.ccl.net> X-Original-From: "jim pfaendtner" Date: Thu, 18 May 2006 14:10:49 -0400 Sent to CCL by: "jim pfaendtner" [pfaendtner:-:northwestern.edu] Hi, I am looking for a copy of TheRate, I have found several links online, but the code doesn't seem to be readily available any longer. Could anyone provide me with a copy of this? thank you. Jim From owner-chemistry@ccl.net Thu May 18 19:25:00 2006 From: "Wai-To Chan chan__curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: TheRate kinetics code Message-Id: <-31782-060518185618-14296-22G/Rq5f0xbq5PJ/13cigw*_*server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 18 May 2006 18:31:38 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan/a\curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<, Hi, I am looking for a copy of TheRate, I have found several links online, but the code doesn't seem to be readily available any longer. Could anyone provide me with a copy of this? thank you. Jim >>>>>>>>>>>>>>> I installed Wendell Duncan's TheRate about 6 years ago. Never got to use it much beyond testing because of some minor problems in its compatibility with the machine I was using. I seem to remember some java scripts were used for running the program but can't remember if it was just the executable image rather than the code that was provided. There must be some kind of license agreement entailed in my acquisition of the program. I can't remember any details but will be very surprised if users other than the authors of the program are free to distribute the code. If what you need is a code for automatic manipulation of Gaussian output for the derivation of kinetic parameters take a look into "Iso-nitrous acid: spectral frequencies and possible synthetic pathways" Phys. Chem. Chem. Phys., 4, 557-560 (2002) by Chan and Pritchard The program used and mentioned in this paper is nowhere as sophisticated as TheRate. It doesn't have a GUI like TheRate but in my view is almost as easy to use. Users only need to input a set of g98 output files and a specified temperature range to obtain the A-factors and activation barrier derived from an Arrhenius plot plus thermochemical quantities. You may contact me if you decide that the program can do what you want. I must point out that development of this program has ceased since this paper was published and I cannot guarantee its distribution. Wai-To Chan From owner-chemistry@ccl.net Thu May 18 20:00:02 2006 From: "Young Leh youngleh-x-gmail.com" To: CCL Subject: CCL: Export Material Studio Structure Message-Id: <-31783-060518190712-14824-M2hcsbV1OYEEwgFvnY747Q!=!server.ccl.net> X-Original-From: "Young Leh" Date: Thu, 18 May 2006 19:07:11 -0400 Sent to CCL by: "Young Leh" [youngleh[A]gmail.com] Dear CCLer, Does anybody know how to export the unit cell strucutres in Material Studio? It looks like if I export the structures to be .PDB format, only very few atoms are exported. Thanks Regards, Young Leh From owner-chemistry@ccl.net Thu May 18 21:00:00 2006 From: "Jan Labanowski janl**speakeasy.net" To: CCL Subject: CCL: NEWLEAD (Linux) uploaded to CCL Archives Message-Id: <-31784-060518205718-30908-ZC30RqnCW/yWeEezLTlCMg|,|server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 19 May 2006 00:57:03 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl^_^speakeasy.net] I would like to thank Vincenzo Tschinke for uploading the NEWLEAD program to CCL Archives today. The program can be retrieved from the following page: http://server.ccl.net/cca/software/LINUX/newlead_linux/ > From the README file: Vincenzo Tschinke and N. Claude Cohen NEWLEAD is a computer program for the automatic generation of candidate structures. The input for the program is a set of fragments in the three-dimensional orientation corresponding to a given pharmacophore model. The treatment consists in connecting the fragments with spacers assembled from small chemical entities (atoms, chains or ring moieties). The results are new structures containing the fragments in the orientation defined in the input. The program offers the opportunity of rapidly applying a pharmacophore model in drug-design by generating automatically a set of chemical sructures conforming to the model. Please upload materials to CCL Archives and share. You can learn how, by visiting the page: http://server.ccl.net/chemistry/aboutccl/supporting/index.shtml Thank you again Vincenzo, CCL Maintainer Jan Labanowski From owner-chemistry@ccl.net Thu May 18 21:34:01 2006 From: "Guilherme Menegon Arantes garantes * iq.usp.br" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31785-060518160314-29203-GNMRUcyRUaIRAk0WnAy9kw.:.server.ccl.net> X-Original-From: Guilherme Menegon Arantes Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 18 May 2006 16:10:41 -0300 MIME-Version: 1.0 Sent to CCL by: Guilherme Menegon Arantes [garantes],[iq.usp.br] On Thu, May 18, 2006 at 01:21:47PM -0400, Ross Walker ross]|[rosswalker.co.uk wrote: > Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk] > > [.....] > before it even starts to become expensive. Plus you can do a simulation with > a full treatment of electrostatics and periodic boundaries for both the QM > and MM regions using PME. Without a PME treatment you will need to use an > infinite (i.e. no) cutoff and probably add an implicit solvent treatment for > the gas phase region of your system to get meaningful results. Using a cut > off with gas phase / water cap simulations introduces serious artefacts into > your simulation and can completely invalidate your results. Hence often it > can be quicker to do a full PME treatment than to run the gas phase > non-periodic simulation. > [.....] I would appreciate if you could point me to any references showing this explicitely. In my experience, properties (say, PMF) calculated in QM/MM simulations with some truncation schemes, in particularly atom-based force-switching, with reasonable cut-off radius, are equivalent to the properties obtained without any truncation. G ______________________________________________________ Dr. Guilherme Menegon Arantes Sao Paulo, Brasil ______________________________________________________ Por favor, note meu novo email: garantes*iq.usp.br Please, note my new email: garantes*iq.usp.br From owner-chemistry@ccl.net Thu May 18 22:09:00 2006 From: "Nathan Scott scottjn-,-gmail.com" To: CCL Subject: CCL: QM/MM computational cost? Message-Id: <-31786-060518215707-30329-R8w/DBiVEzp/ly4wIDIJTw%a%server.ccl.net> X-Original-From: "Nathan Scott" Content-Type: multipart/alternative; boundary="----=_Part_103073_3330678.1148003815778" Date: Thu, 18 May 2006 21:56:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Nathan Scott" [scottjn(_)gmail.com] ------=_Part_103073_3330678.1148003815778 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks to everyone for their help! I appreciate it very much. Ross, thank= s for the insight, as well as the time cost data. You mention that a full ab initio treatment "could get very expensive." I was actually planning to us= e B3LYP/6-31G(d,p), and to do normal mode analysis of the QM system at a few different points in the trajectory. Could you (or anyone else) take a gues= s at how much slower your calculations would have been had you used B3LYP/6-31G(d,p) rather than PM3? Am I right in thinking that the normal mode analysis of the QM system is going to be extremely expensive? J. Nathan Scott Graduate Student University of Pennsylvania Biochemistry and Molecular Biophysics Graduate Group Work Phone: +1.215.898.8783 On 5/18/06, Ross Walker ross]|[rosswalker.co.uk wrote: > > Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk] > Hi Nathan, > > > Greetings CCLers. Can anyone point me to a reference discussing the > > computational cost of QM/MM simulations and how it scales > > with size of the > > components? I have some experience with quantum chemistry > > simulations, as > > well as molecular dynamics simulations, but I'm new to QM/MM > > and am being > > asked as part of a proposal I'm writing to discuss the > > computational cost o=3D > > f > > the calculations I want to do. Right now the plan is to > > solvate a simple 6 > > atom quantum mechanical system with approximately 1000 TIP4P water > > molecules. > > This really depends on the type of QM calculation you plan on doing which > you don't state. Semi-empirical is significantly cheaper than full ab > initio. For what you suggest above if you wanted to do semi-empirical you > can use Amber 9 and the computational cost will be about 6% more than > doing > the calculation classically. You can probably go to about 90 QM atoms or > so > before it even starts to become expensive. Plus you can do a simulation > with > a full treatment of electrostatics and periodic boundaries for both the Q= M > and MM regions using PME. Without a PME treatment you will need to use an > infinite (i.e. no) cutoff and probably add an implicit solvent treatment > for > the gas phase region of your system to get meaningful results. Using a cu= t > off with gas phase / water cap simulations introduces serious artefacts > into > your simulation and can completely invalidate your results. Hence often i= t > can be quicker to do a full PME treatment than to run the gas phase > non-periodic simulation. > > A lot of work has been put into making Amber 9's QM support as fast as > possible while preserving accuracy in the gradients. It is around 10 time= s > quicker than Amber 8 and Charmm c32. The Amber 9 QMMM implementation is > currently being added to Charmm and will I believe be released shortly. > > As a quick guide here are the timings I got for two water molecules > treated > with PM3 and then solvated with a rectangular box consisting of 332 TIP4P > water molecules. PME was run with an 8 angstrom MM and QM direct space cu= t > off, shake was used for both the MM and QM region, langevin thermostating > was used at 300K and a timestep of 2fs was used. For the gas phase > simulation I used an infinite MM and QM cut off. The default SCF > convergence > of 1.0x10-8 KCal/mol was used. > > This is for a pentium-D 3.4GHz 2MB L2 cache machine. Time is for 2000 > steps > =3D 4ps. > > 1 cpu 2 cpu's > time(s) ns/day time(s) ns/day > PME classical =3D 39.99 8.64 23.35 14.80 > PME QMMM =3D 62.15 5.56 40.15 8.83 > Gas phase clas=3D 123.67 2.79 64.48 5.36 > Gas phase QMMM=3D 130.99 2.64 70.12 4.93 > > So for the system you want to study it really won't cost you much at all. > However, if you want to do a full abinitio treatment then it could get > very > expensive. > ------=_Part_103073_3330678.1148003815778 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks to everyone for their help!  I appreciate it very much.  R= oss, thanks for the insight, as well as the time cost data.  You menti= on that a full ab initio treatment "could get very expensive."&nb= sp; I was actually planning to use B3LYP/6-31G(d,p), and to do normal mode = analysis of the QM system at a few different points in the trajectory. = ; Could you (or anyone else) take a guess at how much slower your calculati= ons would have been had you used B3LYP/6-31G(d,p) rather than PM3? &nb= sp; Am I right in thinking that the normal mode analysis of the QM system i= s going to be extremely expensive?

J. Nathan Scott
Graduate Student
University of PennsylvaniaBiochemistry and Molecular Biophysics Graduate Group
Work Phone: +1.21= 5.898.8783


On 5/18/06, Ross Walker ross]|[rosswalker.co.uk= <owner-chemistry]=[ccl.net= > wrote:
Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk]
Hi Nat= han,

> Greetings CCLers.  Can anyone point me to a refe= rence discussing the
> computational cost of QM/MM simulations and ho= w it scales
> with size of the
> components?  I have some experi= ence with quantum chemistry
> simulations, as
> well as molecul= ar dynamics simulations, but I'm new to QM/MM
> and am being
> = asked as part of a proposal I'm writing to discuss the
> computational cost o=3D
> f
> the calculations I want = to do.  Right now the plan is to
> solvate a simple 6
&g= t; atom quantum mechanical system with approximately 1000 TIP4P water
&g= t; molecules.

This really depends on the type of QM calculation you plan on doing= which
you don't state. Semi-empirical is significantly cheaper than ful= l ab
initio. For what you suggest above if you wanted to do semi-empiric= al you
can use Amber 9 and the computational cost will be about 6% more than d= oing
the calculation classically. You can probably go to about 90 QM ato= ms or so
before it even starts to become expensive. Plus you can do a si= mulation with
a full treatment of electrostatics and periodic boundaries for both the= QM
and MM regions using PME. Without a PME treatment you will need to u= se an
infinite (i.e. no) cutoff and probably add an implicit solvent tre= atment for
the gas phase region of your system to get meaningful results. Using a = cut
off with gas phase / water cap simulations introduces serious artefa= cts into
your simulation and can completely invalidate your results. Hen= ce often it
can be quicker to do a full PME treatment than to run the gas phase
= non-periodic simulation.

A lot of work has been put into making Ambe= r 9's QM support as fast as
possible while preserving accuracy in the gr= adients. It is around 10 times
quicker than Amber 8 and Charmm c32. The Amber 9 QMMM implementation is=
currently being added to Charmm and will I believe be released shortly.=

As a quick guide here are the timings I got for two water molecules= treated
with PM3 and then solvated with a rectangular box consisting of 332 TIP= 4P
water molecules. PME was run with an 8 angstrom MM and QM direct spac= e cut
off, shake was used for both the MM and QM region, langevin thermo= stating
was used at 300K and a timestep of 2fs was used. For the gas phase
s= imulation I used an infinite MM and QM cut off. The default SCF convergence=
of 1.0x10-8 KCal/mol was used.

This is for a pentium-D 3.4GHz 2MB L2 cache machine. Time is for 2000 steps
=3D 4ps.

 &nbs= p;            &= nbsp;      1 cpu     &nbs= p;         2 cpu's
  &= nbsp;           &nbs= p;  time(s) ns/day      time(s) ns/dayPME classical =3D   39.99  8.64   &nbs= p;    23.35   14.80
PME QMMM      =3D   62.15 &nbs= p;5.56        40.15  &nbs= p; 8.83
Gas phase clas=3D  123.67  2.79 &n= bsp;      64.48    5.36Gas phase QMMM=3D  130.99  2.64   &nbs= p;    70.12    4.93

So for t= he system you want to study it really won't cost you much at all.
However, if you want to do a full abinitio treatment then it could get = very
expensive.

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