From owner-chemistry@ccl.net Wed Mar 17 00:15:01 2010 From: "Andrew Orry andy]-[molsoft.com" To: CCL Subject: CCL: Protein Structure and Drug Discovery Workshop - April 29th-30th 2010 La Jolla, CA. Message-Id: <-41463-100316201403-433-ar9tBHsI5oWy8YJEwBLwzw(-)server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 16 Mar 2010 15:37:35 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy : molsoft.com] "Protein Structure and Drug Discovery" Workshop - April 29th-30th 2010 La Jolla, CA. Please join us at MolSoft's ( www.molsoft.com ) "Protein Structure and Drug Design" Workshop in La Jolla, California USA. For more information and a registration form see: www.molsoft.com/training.html This workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (University of California San Diego) and Dr. Maxim Totrov (MolSoft). Price: $349 (Academics) $749 (Commercial) The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - How To Display Fully Interactive 3D Molecules in PowerPoint and the Web see: http://www.molsoft.com/activeicm.html - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking Please see our website at www.molsoft.com for more details or E mail: andy(!)molsoft.com or call 858-625-2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Follow us on Twitter: http://twitter.com/MolSoft Latest News: http://www.molsoft.com/news.html From owner-chemistry@ccl.net Wed Mar 17 03:18:00 2010 From: "Peter Khlyabich khlyabic]^[usc.edu" To: CCL Subject: CCL:G: Gaussun 03 multiple nodes Message-Id: <-41464-100317031545-3323-ii+tHa2knB4WMSV54aO/WA[A]server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Wed, 17 Mar 2010 03:15:42 -0400 Sent to CCL by: "Peter Khlyabich" [khlyabic%%usc.edu] Dear colleagues, I'm trying to run Gaussian 03 E01. on multiple nodes. Unfortunately I faced problems. When I run 1 node and 8 processors the calculations are done without problems. As soon as the number of nodes is increased to 2 and more I have problem with communication between the nodes as I suppose. My run file: #running gaussian on hpc #PBS -l walltime=24:00:00 #PBS -l arch=x86_64 #PBS -l nodes=2:ppn=8 cd "$PBS_O_WORKDIR" /usr/usc/gaussian/default/g03/g03 < 10.in > 10.out My input file: %chk=/tmp/freja13172.chk %mem=100MW %NProcShared=8 %LindaWorkers=hpc2525,hpc2526 #T B3LYP/6-31G(d) Opt Int=FMMNAtoms=300 5 units with hydrogens in cis and in iso 0 1 C -5.58481969 0.27508090 0.00000000 C -4.07766969 0.27508090 0.00000000 H -3.70360269 0.82779590 -0.90236800 H -5.97463269 1.32144090 0.00000000 H -5.97835169 -0.24811010 -0.90491000 H -5.97844469 -0.24822410 0.90478800 C -3.51792269 -1.12424710 -0.00007200 H -3.70353069 0.82774090 0.90236400 H -3.85767769 -1.68392810 -0.90496300 C -1.97835960 -1.08756588 -0.00015199 C -1.45997195 -1.75480497 -1.24817737 C -1.45974804 -1.75461457 1.24785588 H -1.67537622 -0.00687673 -0.00034440 H -1.85761202 -1.24325542 -2.15758534 H -0.34423278 -1.71582774 -1.28081571 H -1.77308410 -2.82640901 -1.28066812 H -1.85716152 -1.24299888 2.15729660 H -1.77297354 -2.82621490 1.28046395 C 0.07867044 -1.70095767 1.29245987 C 0.62388763 -3.08990247 1.50476079 C 0.51715341 -0.75509599 2.38081364 H 0.42292686 -1.31199685 0.29753022 H 0.28565398 -3.77067768 0.68685705 H 1.74067253 -3.07712083 1.51406089 H 0.27127107 -3.50649885 2.47920376 H 0.10120350 0.26546832 2.20135698 H 0.16163408 -1.11080209 3.37809993 C 2.05317043 -0.65368643 2.42517354 C 2.54925220 -1.12541207 3.76788681 C 2.47145134 0.76610322 2.14114190 H 2.45044451 -1.32876215 1.62134889 H 2.22706340 -2.17809412 3.95464414 H 3.66453679 -1.08463352 3.81188406 H 2.14371979 -0.48181023 4.58565831 H 2.09262612 1.09181239 1.14255514 H 2.09262612 1.09181239 1.14255514 H 2.06377104 1.45902862 2.91648178 H 3.58472944 0.85617551 2.14283563 C -3.98626967 -1.89601628 1.24757516 C -4.80083796 -3.09083317 0.82284909 C -4.77147873 -0.97324600 2.14388834 H -3.06396140 -2.24375542 1.78433668 H -4.19813895 -3.75808371 0.16076599 H -5.12892342 -3.68004525 1.71315658 H -5.71163411 -2.76744701 0.26311535 H -4.14747510 -0.09743816 2.44447215 H -5.68147139 -0.59457178 1.61851234 H -5.09887074 -1.50732362 3.06859346 1 2 1.0 4 1.0 5 1.0 6 1.0 2 7 1.0 8 1.0 3 1.0 3 4 5 6 7 9 1.0 10 1.0 38 1.0 8 9 10 11 1.0 12 1.0 13 1.0 11 14 1.0 15 1.0 16 1.0 12 17 1.0 18 1.0 19 1.0 13 14 15 16 17 18 19 20 1.0 21 1.0 22 1.0 20 23 1.0 24 1.0 25 1.0 21 26 1.0 27 1.0 28 1.0 22 23 24 25 26 27 28 29 1.0 30 1.0 31 1.0 29 32 1.0 33 1.0 34 1.0 30 35 1.0 36 1.0 37 1.0 31 32 33 34 35 36 37 38 39 1.0 40 1.0 41 1.0 39 42 1.0 43 1.0 44 1.0 40 45 1.0 46 1.0 47 1.0 41 42 43 44 45 46 47 The "O file": Begin PBS Prologue Tue Mar 16 23:04:30 PDT 2010 Job ID: 7754203.hpc-pbs.usc.edu Username: khlyabic Group: m-chem Name: 10_run Queue: main Shared Access: no Nodes: hpc2532 hpc2613 PVFS: /scratch (413G) TMPDIR: /tmp/7754203.hpc-pbs.usc.edu End PBS Prologue Tue Mar 16 23:04:35 PDT 2010 ---------------------------------------- Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. ---------------------------------------- Begin PBS Epilogue Tue Mar 16 23:14:40 PDT 2010 Job ID: 7754203.hpc-pbs.usc.edu Username: khlyabic Group: m-chem Job Name: 10_run Session: 10981 Limits: neednodes=2:ppn=8,nodes=2:ppn=8,walltime=24:00:00 Resources: cput=00:00:06,mem=8480kb,vmem=345032kb,walltime=00:10:05 Queue: main End PBS Epilogue Tue Mar 16 23:14:47 PDT 2010 The error file: Connection closed by 10.125.11.25^M subprocess pid = 11216 has exited. status = 0xff00, id = 0, state = 13. command was /usr/usc/gaussian/g03-E01/g03/linda7.2/opteron-linux-I8/bin/linda_rsh hpc2525-e0.usc.edu -r ssh /usr/usc/gaussian/g03-E01/g03/linda-exe/l302.exel 104857600 /tmp/freja13172.chk 1 /tmp/Gau-11176.int 0 /tmp/Gau-11176.rwf 0 /tmp/Gau-11176.d2e 0 /tmp/Gau-11176.scr 0 /tmp/Gau-11175.inp 0 junk.out 0 +LARGS 0 hpc2525-e0.usc.edu 10.125.11.113 35041 1 1 /auto/rcf-proj3/bct/khlyabic/gaussian/tests died without ever signing in Sign in timed out after 0 worker connections. Did not reach minimum (1), shutting down. I would appreciate any help with running on several nodes. Thanks in advance Peter From owner-chemistry@ccl.net Wed Mar 17 04:02:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom,+,gmail.com" To: CCL Subject: CCL: "Fork" and "Wait" commands.. Message-Id: <-41465-100317040032-7688-fiEbAZGe9n//KFifYUHeUg_._server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Mar 2010 09:00:12 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom(0)gmail.com] > Does anyone know of any Linux fortran compilers that have both the "wait" and > "fork" commands? If you don't find such a compiler you can easily write a wrapper in C and link that to your fortran program, i.e. (untested) #include #include #include int fork_(void) { return fork(); } int wait_(int *status) { return wait(status); } Sincerely, Ulf Ekstrom From owner-chemistry@ccl.net Wed Mar 17 04:39:01 2010 From: "Vladimir Chupakhin chupvl||gmail.com" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41466-100317032741-24133-NRYsRkm/Ng46QJeBdKGX1w(~)server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sat, 02 Jan 2010 09:33:48 +0300 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl(_)gmail.com] Note to all russian speaking reader of CCL. Group of molecular modeling and QSAR of Moscow State University have translated Molecular modelling: principles and applications to Russian language (Молекулярное моделирование Теория и практика, Издательство Бином). Vladimir Chupakhin, Dpt. of Chemistry, Moscow State University, Moscow, Russia On 15.03.2010 23:56, Barbault Florent florent.barbault*_*univ-paris-diderot.fr wrote: > > Sent to CCL by: "Barbault Florent" > [florent.barbault/./univ-paris-diderot.fr] > Hi, > > Personnaly, I found the book "molecular modelling: principles and > applications" very useful... Here is the link on amazon (I have no > interest on this book!) > > http://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp/0582382106/ref=sr_1_1?ie=UTF8&s=books&qid=1268686522&sr=8-1 > > > Best regards > Florent Barbault > > > On Mon, 15 Mar 2010 15:35:39 -0400 > "Senthil Natesan sen.natesan]^[yahoo.com" > wrote: >> >> Sent to CCL by: "Senthil Natesan" [sen.natesan,yahoo.com] >> Dear All, >> >> Greetings. It will be very helpful if you could recommend a few >> essential (authoritative in its area) books in the following areas >> >> 1) Molecular dynamics simulation >> 2) Molecular recognition >> 3) QM/MM calculations >> 4) QSAR >> 5) ADMET >> >> Books published after 2000 would be great as it would cover the >> latest developments. >> >> Thanks everyone for your time and valuable recommendations. >> >> Senthil Natesan,>> To recover the email address of the author of the message, please >> change> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/> > > ------------------------------------------------- > Dr Florent Barbault > Maitre de conferences / Assistant professor > > Universite Paris Diderot > Laboratoire ITODYS > 15 rue Jean de Baïf, bâtiment Lavoisier > 75013 Paris FRANCE > http://www.itodys.univ-paris7.fr/ > tel : (33) 01-57-27-88-50 > e-mail : florent.barbault=univ-paris-diderot.fr > ------------------------------------------------- > From owner-chemistry@ccl.net Wed Mar 17 06:33:00 2010 From: "huixiaokang328 ~ 163.com" To: CCL Subject: CCL: problem on g09 Message-Id: <-41467-100317045317-29526-l0o1/zYzWwGvVfzY6L4t+Q]-[server.ccl.net> X-Original-From: huixiaokang328-#-163.com Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Wed, 17 Mar 2010 16:07:25 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: huixiaokang328||163.com Dear PS: I have tried it in your way again ,but failed .Do you have ahother advice t= o solve this problem? Thank you very much! Best wishes! xkang

=E5=9C=A82010-03-16 14:33:46=EF=BC=8C"Prasenjit.Seal#%#crm2.uh= p-nancy.fr" =E5=86=99=E9=81=93=EF=BC=9A > >Sent to CCL by: Prasenjit.Seal%x%crm2.uhp-nancy.fr >Selon "Xiaohui Kang huixiaokang328::163.com" : > >> >> Sent to CCL by: "Xiaohui Kang" [huixiaokang328 ~~ 163.com] >> Dear CCL Subscribers >> When I compute the thermochemistry of water at both 298.15K and 373K i= n an >> input file with g09,I can not get the information on 373K ,that is to sa= y,the >> "--Link--" does not play a role in my calculation.The following is my in= put >> file : >> >> %Chk=3Dwatertest.chk >> %nproc=3D8 >> #T RHF/6-31G(d) Freq=3Dnoraman >> water298 >> >> 0 1 >> O 0.00000000 0.00000000 0.11980000 >> H 0.00000000 0.76140000 -0.47910000 >> H 0.00000000 -0.76140000 -0.47910000 >> >> --Link1-- >> %Chk=3Dwatertest.chk >> %nproc=3D8 >> #T RHF/6-31G(d) Geom=3DCheck Freq=3DReadFC Guess=3DRead Test >> >> water373 >> >> 0 1 >> >> 373.0 1.0 0.9 >> 16 >> 1 >> 1 >> Can anybody tell me what is the reason resulting in this phenomenon? >> >> Sincerely >> >> xkang> >> >> > > >Dear Prof. Kang, > >You can try it by writting "Temperature=3D373" in the route section of the= second >link instead of writting it in one of the bottom lines. > >Regards, >PS > > > >-=3D This is automatically added to each message by the mailing script =3D= -> >Subscribe/Unsubscribe:=20> >Job: http://www.ccl.net/jobs=20> > From owner-chemistry@ccl.net Wed Mar 17 07:07:01 2010 From: "Daniil Bratashov dn2010-x-gmail.com" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41468-100317061040-4610-48I3mMBZGFFlBr2hE6JfTA===server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=KOI8-R Date: Wed, 17 Mar 2010 13:10:02 +0300 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010=-=gmail.com] On Sat, 02 Jan 2010 09:33:48 +0300 "Vladimir Chupakhin chupvl||gmail.com" wrote: > Note to all russian speaking reader of CCL. Group of molecular > modeling and QSAR of Moscow State University have translated > Molecular modelling: principles and applications to Russian language > ( , ). Seems that it's translation of another book, not one written by Leach A.R. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Wed Mar 17 07:42:01 2010 From: "Andreea Cristina Balaceanu abalaceanu*_*yahoo.com" To: CCL Subject: CCL:G: Flory interaction parameter estimation using G03 Message-Id: <-41469-100317064419-11485-WFClny3615vpaWI5NX71kg]-[server.ccl.net> X-Original-From: "Andreea Cristina Balaceanu" Date: Wed, 17 Mar 2010 06:44:15 -0400 Sent to CCL by: "Andreea Cristina Balaceanu" [abalaceanu(-)yahoo.com] Hello, I am a PhD student and I want to use the Gaussian 03 program to estimate the Flory interaction parameter between a copolymer and water. I know that the Flory interaction parameter is given by: X= z/kT[E_12 - 1/2(E_11 + E_22), where X is the Flory interaction parameter, z is the coordination number, E_12 is the interaction energy between monomer and water, E_11 is the interaction energy between water molecules, and E_22 is the interaction energy between monomers. I now that you can calculate the interaction energy in the Gaussian program by using E_interaction= E_AB,bAB - E_A,bAB - E_B,bAB, where bAB refers to the basis set. My questions are: Can I estimate the Flory interaction parameter in this way? How exactly do I calculate E_AB? Do I just put a monomer next to a water molecule and compute the minimal potential energy? The water molecules interact with the polymer by hydrogen bondings, so do I set the distance between my monomer and the water molecule of the order of a hydrogen bond? Thank you very much in advance for your help. Andreea Balaceanu. From owner-chemistry@ccl.net Wed Mar 17 08:54:00 2010 From: "Justin Finnerty justin.finnerty|a|uni-oldenburg.de" To: CCL Subject: CCL:G: Gaussian03/09 and Infiniband Message-Id: <-41470-100316123714-25878-jHTzCSFHZ8ys4bEkCZBC+g[]server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 16 Mar 2010 16:22:04 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty-$-uni-oldenburg.de] On Tue, 2010-03-16 at 04:48 -0400, Chris Perry christopher.perry2#% #wits.ac.za wrote: > Sent to CCL by: "Chris Perry" [christopher.perry2===wits.ac.za] > Dear colleagues > > We have have built a small cluster of computers that run G03 and G09 under Linux. > Currently we are using standard 1-gigabit ethernet networking to interconnect the nodes, > but are looking to upgrad this. A bit of research on the net has revealed that Infiniband > seems to be the way to go. My question is does Gaussian (or rather TCP-Linda) support > Infiniband? Would I need to obtain new G03/G09 binaries to get the networking to work, > or would it be handled naitively by the operating system? > We also have a cluster for running Gaussian with gigabit ethernet and thought about upgrading to infiniband. However we had a chance to try Gaussian on another cluster that had infiniband. TCP-linda does not support infiniband so we first used the standard gigabit ethernet and then used the infiniband as the network interconnect. Our results where that infiniband makes no difference to Gaussian (in our test using the infiniband was slightly slower!) This is not surprising as Gaussian is optimised to use very low network bandwidth anyway. Our final decision was to invest in more memory and nodes! Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Mar 17 09:29:01 2010 From: "Igor Filippov Contr igorf++helix.nih.gov" To: CCL Subject: CCL:G: unix based workstation Message-Id: <-41471-100317000250-25645-uwJjxEtvE2mKvXIJ7Xrolw*server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 16 Mar 2010 22:39:27 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf*|*helix.nih.gov] For this amount you can buy several and it'll probably do you most gain for your money if you're planning to run several jobs simultaneously. I would buy ~10-15 desktops from cyberpowerpc.com and set up a small linux cluster. If you need something more ready-made check out penguincomputing.com Igor On Tue, 2010-03-16 at 16:57 -0400, Adel El-Azhary azhary[-]ksu.edu.sa wrote: > Sent to CCL by: "Adel El-Azhary" [azhary ~ ksu.edu.sa] > Dear All: > > We are interested to buy a UNIX based workstation or server in the price range of $8-20k mainly to run Gaussian jobs. Any informations on what brand or a model to buy with approximate price are greatly appreciated. > > Best regards, > > Adel El-Azhary> > -- Igor Filippov [Contr] From owner-chemistry@ccl.net Wed Mar 17 10:04:00 2010 From: "Christopher Perry Christopher.Perry2..wits.ac.za" To: CCL Subject: CCL:G: input to generate wave function file Message-Id: <-41472-100317015035-28625-oChJ9O9cemrHYn93k0dU4w-$-server.ccl.net> X-Original-From: "Christopher Perry" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 17 Mar 2010 07:08:50 +0200 MIME-Version: 1.0 Sent to CCL by: "Christopher Perry" [Christopher.Perry2+*+wits.ac.za] Dear=20Satyajit You=20need=20to=20include=20the=20command=20"out=3Dwfn"=20in=20the=20rout= e=20section=20of=20the input=20file,=20and=20then=20the=20filename=20that=20you=20want=20to=20us= e=20right=20at=20the=20end. For=20example: #P=20B3LYP/6-31+G(d)=20Scf=3Dtight=20int=3Dultrafine=20out=3Dwfn=20test ...Comments ...Charge=20and=20multiplicity ....Z-matrix ... ... ... Filename.wfn Regards Chris Christopher=20B.=20Perry,=20PhD Lecturer,=20School=20of=20Chemistry University=20of=20the=20Witwatersrand PO=20Wits,=20Johannesburg 2050,=20South=20Africa Tel=20+27=20+11=20717=206732 Fax=20+27=20+11=20717=206749=20 -----Original=20Message----- > From:=20owner-chemistry+christopher.perry2=3D=3Dwits.ac.za- -ccl.net [mailto:owner-chemistry+christopher.perry2=3D=3Dwits.ac.za- -ccl.net]=20On Behalf=20Of=20Mr.=20Satyajit=20Sarmah=20satyacs{=3D}tezu.ernet.in Sent:=2015=20March=202010=2003:49=20PM To:=20Christopher=20Perry Subject:=20CCL:G:=20input=20to=20generate=20wave=20function=20file Sent=20to=20CCL=20by:=20"Mr.=20Satyajit=20Sarmah"=20[satyacs|a|tezu.ernet= .in] Hi=20everyone =20I=20am=20using=20Gaussian=2003=20.=20I=20wanted=20know=20the=20require= d=20input=20to=20generate wave=20function=20file=20using=20Gaussian03.=20If=20anybody=20can=20give= =20solution=20in this regard. =20Thanks. Satyajit. ___________________ D=20I=20S=20C=20L=20A=20I=20M=20E=20R This=20e-mail=20may=20contain=20privileged=20information=20and=20is=20int= ended=20solely for the=20individual=20named.=20If=20you=20are=20not=20the=20named=20addresse= e=20you=20should=20not disseminate,=20distribute=20or=20copy=20this=20e-mail.=20Please=20notify= =20the=20sender immediately=20by=20e-mail=20if=20you=20have=20received=20this=20e-mail=20= in=20error=20and destroy=20it=20from=20your=20system.=20Though=20considerable=20effort=20h= as=20been=20made=20to deliver=20error=20free=20e-mail=20messages=20but=20it=20can=20not=20be=20= guaranteed=20to=20be secure=20 or=20error-free=20as=20information=20could=20be=20intercepted,=20corrupte= d,=20lost, destroyed,=20 delayed,=20or=20may=20contain=20viruses.=20The=20recipient=20must=20verif= y=20the=20integrity of=20 this=20e-mail=20message. -=3D=20This=20is=20automatically=20added=20to=20each=20message=20by=20the= =20mailing=20script=20=3D- To=20recover=20the=20email=20address=20of=20the=20author=20of=20the=20mes= sage,=20please=20change the=20strange=20characters=20on=20the=20top=20line=20to=20the=20- -=20sign.= =20You=20can=20also look=20up=20the=20X-Original-From:=20line=20in=20the=20mail=20header. E-mail=20to=20subscribers:=20CHEMISTRY- -ccl.net=20or=20use: =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail=20to=20administrators:=20CHEMISTRY-REQUEST- -ccl.net=20or=20use =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=20 =20=20=20=20=20=20http://www.ccl.net/chemistry/sub_unsub.shtml Before=20posting,=20check=20wait=20time=20at:=20http://www.ccl.net Job:=20http://www.ccl.net/jobs=20 Conferences:=20http://server.ccl.net/chemistry/announcements/conferences/ Search=20Messages:=20http://www.ccl.net/chemistry/searchccl/index.shtml If=20your=20mail=20bounces=20from=20CCL=20with=205.7.1=20error,=20check: =20=20=20=20=20=20http://www.ccl.net/spammers.txt RTFI:=20http://www.ccl.net/chemistry/aboutccl/instructions/

This=20communication=20is=20intended=20for=20the=20addressee= =20only.=20It=20is=20confidential.=20If=20you=20have=20received=20this=20= communication=20in=20error,=20please=20notify=20us=20immediately=20and=20= destroy=20the=20original=20message.=20You=20may=20not=20copy=20or=20disse= minate=20this=20communication=20without=20the=20permission=20of=20the=20U= niversity.=20Only=20authorized=20signatories=20are=20competent=20to=20ent= er=20into=20agreements=20on=20behalf=20of=20the=20University=20and=20reci= pients=20are=20thus=20advised=20that=20the=20content=20of=20this=20messag= e=20may=20not=20be=20legally=20binding=20on=20the=20University=20and=20ma= y=20contain=20the=20personal=20views=20and=20opinions=20of=20the=20author= ,=20which=20are=20not=20necessarily=20the=20views=20and=20opinions=20of= =20The=20University=20of=20the=20Witwatersrand,=20Johannesburg.=20All=20a= greements=20between=20the=20University=20and=20outsiders=20are=20subject= =20to=20South=20African=20Law=20unless=20the=20University=20agrees=20in= =20writing=20to=20the=20contrary.

From owner-chemistry@ccl.net Wed Mar 17 10:39:01 2010 From: "andras.borosy+/-givaudan.com" To: CCL Subject: CCL:G: unix based workstation Message-Id: <-41473-100317043442-15796-p57myq/Tri41XiyWvdlh7A_._server.ccl.net> X-Original-From: andras.borosy-,-givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002C18D2C12576E9_=" Date: Wed, 17 Mar 2010 09:01:40 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy-x-givaudan.com This is a multipart message in MIME format. --=_alternative 002C18D2C12576E9_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Adel, I do not know if you insist on Gaussian (which is the slowest QC package, = I have ever used). If not, you may try the following architectures: http://www.petachem.com/index.html or http://www.pqs-chem.com/products.shtml Best wishes, Andr=E1s=20 "Adel El-Azhary azhary[-]ksu.edu.sa" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com(0)ccl.net 16.03.2010 21:57 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL:G: unix based workstation Sent to CCL by: "Adel El-Azhary" [azhary ~ ksu.edu.sa] Dear All: We are interested to buy a UNIX based workstation or server in the price=20 range of $8-20k mainly to run Gaussian jobs. Any informations on what=20 brand or a model to buy with approximate price are greatly appreciated. Best regards, Adel El-Azhary -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 002C18D2C12576E9_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Adel,

I do not know if you insist on Gauss= ian  (which is the slowest QC package, I have ever used).

If not, you may try the following ar= chitectures:

http://www.petachem.com/index.html

or

http://www.pqs-chem.com/products.sht= ml

Best wishes,

Andr=E1s




"Adel El-Azhary = azhary[-]ksu.edu.sa" <owner-chemistry(0)ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com(0)ccl.net

16.03.2010 21:57
Please respond to
"CCL Subscribers" <chemistry(0)ccl.net>
To
"Borosy, Andras " <andras.borosy(0)givaudan.com>
cc
Subject
CCL:G: unix based workstation=






Sent to CCL by: "Adel  El-Azhary" [azhary ~ ksu.edu.sa]
Dear All:

We are interested to buy a UNIX based workstation or server in the price range of $8-20k mainly to run Gaussian jobs. Any informations on what brand or a model to buy with approximate price are greatly appreciated.

Best regards,

Adel El-Azhary



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
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     http://www.ccl.net/chemistry/sub=5Funsub.shtml
     http://www.ccl.net/spammers.txt
--=_alternative 002C18D2C12576E9_=-- From owner-chemistry@ccl.net Wed Mar 17 11:14:01 2010 From: "Prasenjit.Seal-$-crm2.uhp-nancy.fr" To: CCL Subject: CCL:G: input to generate wave function file Message-Id: <-41474-100317022134-30930-HUxe212LcWIrK3mOVXVbIA(a)server.ccl.net> X-Original-From: Prasenjit.Seal : crm2.uhp-nancy.fr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Mar 2010 07:21:20 +0100 MIME-Version: 1.0 Sent to CCL by: Prasenjit.Seal a crm2.uhp-nancy.fr Selon "Mr. Satyajit Sarmah satyacs{=}tezu.ernet.in" : > > Sent to CCL by: "Mr. Satyajit Sarmah" [satyacs|a|tezu.ernet.in] > Hi everyone > > I am using Gaussian 03 . I wanted know the required input to generate > wave function file using Gaussian03. If anybody can give solution in this > regard. > > Thanks. > Satyajit. > > > > ___________________ > D I S C L A I M E R > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and > destroy it from your system. Though considerable effort has been made to > deliver error free e-mail messages but it can not be guaranteed to be secure > or error-free as information could be intercepted, corrupted, lost, > destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message.> > > Dear Satyajit, You have to give "output=wfn" in the route section and after the end of the input, i.e., the last line of the input file, you have to specify "filename.wfn" (where filename is your desired wfn file) preceeded by a blank line. Cheers, PS From owner-chemistry@ccl.net Wed Mar 17 11:48:01 2010 From: "Daniel Tunega daniel.tunega-.-univie.ac.at" To: CCL Subject: CCL: Hydrogen bond analysis Message-Id: <-41475-100316121147-10227-9N2ibROBQDE+5nCBqjQjIg/./server.ccl.net> X-Original-From: "Daniel Tunega" Date: Tue, 16 Mar 2010 12:11:43 -0400 Sent to CCL by: "Daniel Tunega" [daniel.tunega__univie.ac.at] Hello all, can anybody recommend a program (preferentially open source) doing a hydrogen bond analysis (e.g. average No. of H-bonds/molecule, etc.) on MD/MC outputs (format of output file is not a key problem). Thanks, Daniel From owner-chemistry@ccl.net Wed Mar 17 12:23:01 2010 From: "Andreas Klamt klamt_-_cosmologic.de" To: CCL Subject: CCL:G: Flory interaction parameter estimation using G03 Message-Id: <-41476-100317094143-15892-Rb45Aoz+evXrKcr/2+DBLA .. server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 17 Mar 2010 14:41:29 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt_+_cosmologic.de] Dear Andreea, I am afraid that what you are describing here does not make much sense. The Flory or Flory-Huggins interaction parameters are effective interaction parameters in the bulk liquid phase. And what you express as E in the formulas should be a free energy, not an interaction enthalpy. They have little to do with the interaction energies, which you get when you optimize pairs of molecules. Such pair would just probe some optimally strong interactions at a small portion of the surface, but in a liquid the molecules are interacting everywhere. Some of our industrial customers are using our COSMO-RS method/COSMOtherm program to calculate Flory-Huggins parameters, making use of the chemical potentials of the two compounds in the 2 liquid phases calculted by COSMOtherm. Indeed, we also have developed a special tool (COSMOmeso) to set up the required DFT/COSMO and COSMOtherm calculations. Alternative methods might be force-field based MD or MC simulations or ab-initio-MD (Car-Parrinello) simulations, but they are not simple, and COSMO-RS usually is more accurate (see the industrial fluid property simuation challenge)than the force-field based simulations, and I doubt that you will be able to afford the calculation times required for abinitio MD. If you are lucky and have an older version of G03 (check for the existance of the keyword COSMORS) then you can do the required DFT/COSMO calculations with G03. But you will need a COSMO-RS program, e.g. our COSMOtherm, to do the thermodynamic postprocessing. Best regards Andreas Andreea Cristina Balaceanu abalaceanu*_*yahoo.com schrieb: > Sent to CCL by: "Andreea Cristina Balaceanu" [abalaceanu(-)yahoo.com] > Hello, > > I am a PhD student and I want to use the Gaussian 03 program to estimate the Flory interaction parameter between a copolymer and water. I know that the Flory interaction parameter is given by: X= z/kT[E_12 - 1/2(E_11 + E_22), where X is the Flory interaction parameter, z is the coordination number, E_12 is the interaction energy between monomer and water, E_11 is the interaction energy between water molecules, and E_22 is the interaction energy between monomers. > > I now that you can calculate the interaction energy in the Gaussian program by using E_interaction= E_AB,bAB - E_A,bAB - E_B,bAB, where bAB refers to the basis set. > > My questions are: > Can I estimate the Flory interaction parameter in this way? > How exactly do I calculate E_AB? Do I just put a monomer next to a water molecule and compute the minimal potential energy? The water molecules interact with the polymer by hydrogen bondings, so do I set the distance between my monomer and the water molecule of the order of a hydrogen bond? > > Thank you very much in advance for your help. > > Andreea Balaceanu.> > > > From owner-chemistry@ccl.net Wed Mar 17 12:58:00 2010 From: "Lev Gorenstein lev[*]ledorub.poxod.com" To: CCL Subject: CCL:G: Gaussian03/09 and Infiniband Message-Id: <-41477-100317115046-28145-1SMmjSR6vkaPLadYLEu52Q|-|server.ccl.net> X-Original-From: Lev Gorenstein Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 17 Mar 2010 11:50:35 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Lev Gorenstein [lev^^ledorub.poxod.com] On Tue, 16 Mar 2010, Justin Finnerty justin.finnerty|a|uni-oldenburg.de wrote: JFj> We also have a cluster for running Gaussian with gigabit ethernet and JFj> thought about upgrading to infiniband. However we had a chance to try JFj> Gaussian on another cluster that had infiniband. TCP-linda does not JFj> support infiniband so we first used the standard gigabit ethernet and JFj> then used the infiniband as the network interconnect. Our results where JFj> that infiniband makes no difference to Gaussian (in our test using the JFj> infiniband was slightly slower!) Not exactly Gaussian-related, but my experience with CHARMM on Infiniband has been mostly disappointing. When it runs, it scales indeed better than plain GigE, but quite often it crashes, not all nodes/ppn combinations are robust, etc. Granted, CHARMM is a beast in itself, and I didn't spend enough time figuring out how the problems are partitioned between CHARMM, Infiniband and specifics of our local setup. On the other hand, we had a pretty good success with 10 GigE interconnects, which is in the same price and performance range as Infiniband. So this may be a nice route to choose. JFj> This is not surprising as Gaussian is optimised to use very low network JFj> bandwidth anyway. Our final decision was to invest in more memory and JFj> nodes! What about latency? Regards, Lev -- Note that you do not need a parachute to sky-dive. You need a parachute to sky-dive twice. From owner-chemistry@ccl.net Wed Mar 17 13:33:00 2010 From: "Jason Swails jason.swails---gmail.com" To: CCL Subject: CCL:G: Gaussun 03 multiple nodes Message-Id: <-41478-100317115217-29326-NOMRagMlHv97xt5EuExcvQ%x%server.ccl.net> X-Original-From: Jason Swails Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Mar 2010 11:21:48 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails!A!gmail.com] On Wed, Mar 17, 2010 at 3:15 AM, Peter Khlyabich khlyabic]^[usc.edu wrote: > > Sent to CCL by: "Peter =A0Khlyabich" [khlyabic%%usc.edu] > Dear colleagues, > > I'm trying to run Gaussian 03 E01. on multiple nodes. Unfortunately I fac= ed problems. When I run 1 node and 8 processors the calculations are done w= ithout problems. As soon as the number of nodes is increased to 2 and more = I have problem with communication between the nodes as I suppose. Gaussian parallel engine is LINDA, which is strictly shared memory parallelization. Thus, it should only run on a single node (multiple nodes would be operating in a distributed memory parallel environment as opposed to shared memory). I believe that NWChem and (maybe?) QChem operate using MPI and distributed memory. Good luck! Jason --=20 --------------------------------------- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 From owner-chemistry@ccl.net Wed Mar 17 14:08:01 2010 From: "Jason Swails jason.swails-.-gmail.com" To: CCL Subject: CCL: Hydrogen bond analysis Message-Id: <-41479-100317122007-20240-LcGpFIc45uGYSkfShCiqtw . server.ccl.net> X-Original-From: Jason Swails Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Mar 2010 12:19:55 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails],[gmail.com] On Tue, Mar 16, 2010 at 12:11 PM, Daniel Tunega daniel.tunega-.-univie.ac.at wrote: > > Sent to CCL by: "Daniel =A0Tunega" [daniel.tunega__univie.ac.at] > > > Hello all, > > can anybody recommend a program (preferentially open source) > doing a hydrogen bond analysis (e.g. average No. of H-bonds/molecule, etc= .) > on MD/MC outputs (format of output file is not a key problem). > > Thanks, > Daniel ptraj as a part of AmberTools does this. You can get the source and manual from www.ambermd.org . Note that while Amber is not open source (~$400 for an academic license to the source code), AmberTools is GPL. Good luck! Jason > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =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> > > --=20 --------------------------------------- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 From owner-chemistry@ccl.net Wed Mar 17 14:43:00 2010 From: "Mihaly Mezei Mihaly.Mezei.:.mssm.edu" To: CCL Subject: CCL: Hydrogen bond analysis Message-Id: <-41480-100317142723-30110-Ii1/JNW9XCKJtAQwiGP20A+/-server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Wed, 17 Mar 2010 12:28:49 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei]^[mssm.edu] ----- Original Message ----- > From: "Daniel Tunega daniel.tunega-.-univie.ac.at" Date: Tuesday, March 16, 2010 12:11 pm Subject: CCL: Hydrogen bond analysis > > Sent to CCL by: "Daniel Tunega" [daniel.tunega__univie.ac.at] > > > Hello all, > > can anybody recommend a program (preferentially open source) > doing a hydrogen bond analysis (e.g. average No. of H- > bonds/molecule, etc.) > on MD/MC outputs (format of output file is not a key problem). > My program Simulaid (free to academics) does a number of H-bond analyses: http://inka.mssm.edu/~mezei/simulaid (backup site: http://atlas.physbio.mssm.edu/~mezei/simulaid Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Wed Mar 17 15:54:01 2010 From: "Jamin Krinsky jamink!A!berkeley.edu" To: CCL Subject: CCL:G: Gaussun 03 multiple nodes Message-Id: <-41481-100317155219-24162-Mo6mZM+3VSUDMPpi0b+l2Q%x%server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=000e0cd1a992e9a0310482045b2d Date: Wed, 17 Mar 2010 12:45:40 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink . berkeley.edu] --000e0cd1a992e9a0310482045b2d Content-Type: text/plain; charset=ISO-8859-1 Dear Jason, Peter, LINDA is the engine for running Gaussian in network parallel, we used to use it in our facility. G03 (linux at least) will run shared-memory (one node) parallel without LINDA (that's what we are currently doing). Gaussian doesn't come with LINDA, you have to buy it for extra $. Peter either doesn't have LINDA or the cluster/queue/parallel environment is not set up correctly (LINDA has it's own interfacing system so the mpi implementation shouldn't be the problem). Keep in mind that in G03 many job types are not network (e.g. LINDA) parallelizable. Regards, Jamin On Wed, Mar 17, 2010 at 8:21 AM, Jason Swails jason.swails---gmail.com < owner-chemistry]|[ccl.net> wrote: > > Sent to CCL by: Jason Swails [jason.swails!A!gmail.com] > On Wed, Mar 17, 2010 at 3:15 AM, Peter Khlyabich khlyabic]^[usc.edu > wrote: > > > > Sent to CCL by: "Peter Khlyabich" [khlyabic%%usc.edu] > > Dear colleagues, > > > > I'm trying to run Gaussian 03 E01. on multiple nodes. Unfortunately I > faced problems. When I run 1 node and 8 processors the calculations are done > without problems. As soon as the number of nodes is increased to 2 and more > I have problem with communication between the nodes as I suppose. > > Gaussian parallel engine is LINDA, which is strictly shared memory > parallelization. Thus, it should only run on a single node (multiple > nodes would be operating in a distributed memory parallel environment > as opposed to shared memory). I believe that NWChem and (maybe?) > QChem operate using MPI and distributed memory. > > Good luck! > Jason > > -- > --------------------------------------- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > > > > - This is automatically added to each message by the mailing script -> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink]|[berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --000e0cd1a992e9a0310482045b2d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jason, Peter,
LINDA is the engine for running Gaussian in network p= arallel, we used to use it in our facility. G03 (linux at least) will run s= hared-memory (one node) parallel without LINDA (that's what we are curr= ently doing). Gaussian doesn't come with LINDA, you have to buy it for = extra $. Peter either doesn't have LINDA or the cluster/queue/parallel = environment is not set up correctly (LINDA has it's own interfacing sys= tem so the mpi implementation shouldn't be the problem). Keep in mind t= hat in G03 many job types are not network (e.g. LINDA) parallelizable.
Regards,
Jamin


On Wed, Mar 17, 201= 0 at 8:21 AM, Jason Swails jason.swails---gmail.com <owner-chemistry]|[ccl.net<= /a>> wrote:

Sent to CCL by: Jason Swails [jason.swails!A!gmail.com]
On Wed, Mar 17, 2010 at 3:15 AM, Peter Khlyabich khlyabic]^[usc.edu
<owner-chemistry:ccl.net> wrote:
>
> Sent to CCL by: "Peter =A0Khlyabich" [khlyabic%%usc.edu]
> Dear colleagues,
>
> I'm trying to run Gaussian 03 E01. on multiple nodes. Unfortunatel= y I faced problems. When I run 1 node and 8 processors the calculations are= done without problems. As soon as the number of nodes is increased to 2 an= d more I have problem with communication between the nodes as I suppose.
Gaussian parallel engine is LINDA, which is strictly shared memory
parallelization. =A0Thus, it should only run on a single node (multiple
nodes would be operating in a distributed memory parallel environment
as opposed to shared memory). =A0I believe that NWChem and (maybe?)
QChem operate using MPI and distributed memory.

Good luck!
Jason

--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032



--
Jamin L Kri= nsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall,= University of California, Berkeley, CA 94720
jamink]|[berkeley.edu, 510-643-0616
http://glab.cc= hem.berkeley.edu

--000e0cd1a992e9a0310482045b2d-- From owner-chemistry@ccl.net Wed Mar 17 17:06:00 2010 From: "Elaine Meng meng|*|cgl.ucsf.edu" To: CCL Subject: CCL: Monomer to Trimer Message-Id: <-41482-100317125953-21597-TJjCMeq95SrxTDE3rSAUpg:_:server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 17 Mar 2010 12:59:49 -0400 Sent to CCL by: "Elaine Meng" [meng-.-cgl.ucsf.edu] Hi Nahren, Many different programs can build a multimer from the monomer using matrix information in the PDB file. The matrix information can be in SMTRY, CRYST, MTRIX, and BIOMT lines in the file. Ideally the authors would have put information on how to make the trimer in the BIOMT lines, but in this structure 2WKF that information is not included. Instead you can use the SMTRY information in the file to create the whole unit cell, which includes several trimers, and then get rid of all of the extra chains. Another confusing thing about this structure is that it does have two copies of the structure, chains A and B. When you create the unit cell, only the A chains of the different copies form the trimers. The program I work with is Chimera. To do this in Chimera: - fetch 2wkf from the PDB (File... Fetch by ID) - Select chain B, remove it with Actions... Atoms/Bonds... delete - start Unit Cell (under Tools... Higher-Order Structure) - on that tool, click Make Copies, which will give 4 trimers Or you could make the copies first, and then delete chain B (multiple copies) but that would be messier. Chimera can be downloaded free of charge for any noncommercial use. http://www.cgl.ucsf.edu/chimera/index.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Wed Mar 17 17:41:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler##nhlbi.nih.gov" To: CCL Subject: CCL:G: Gaussian03/09 and Infiniband Message-Id: <-41483-100317162216-6047-b5YGQwyATRvUnqjGzXRnkQ---server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 17 Mar 2010 14:48:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler]*[nhlbi.nih.gov] We've had fairly good success with CHARMM on Infiniband, both the PathScale= /Q-Logic product, and newer stuff using OpenIB. We have 100s of nodes usin= g these hardware and software combinations. We have observed some cabling = issues; one of the Infiniband cable connector types in common usage doesn't= seat very well, esp. on some high density switches. Infiniband performs m= uch better that 10 GigE; it's really no comparison, in part due to the late= ncy inherent in both ethernet and TCP protocols. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 3/17/10 10:50 AM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Sent to CCL by: Lev Gorenstein [lev^^ledorub.poxod.com] On Tue, 16 Mar 2010, Justin Finnerty justin.finnerty|a|uni-oldenburg.de wro= te: JFj> We also have a cluster for running Gaussian with gigabit ethernet and JFj> thought about upgrading to infiniband. However we had a chance to try JFj> Gaussian on another cluster that had infiniband. TCP-linda does not JFj> support infiniband so we first used the standard gigabit ethernet and JFj> then used the infiniband as the network interconnect. Our results whe= re JFj> that infiniband makes no difference to Gaussian (in our test using the JFj> infiniband was slightly slower!) Not exactly Gaussian-related, but my experience with CHARMM on Infiniband has been mostly disappointing. When it runs, it scales indeed better than plain GigE, but quite often it crashes, not all nodes/ppn combinations are robust, etc. Granted, CHARMM is a beast in itself, and I didn't spend enough time figuring out how the problems are partitioned between CHARMM, Infiniband and specifics of our local setup. On the other hand, we had a pretty good success with 10 GigE interconnects, which is in the same price and performance range as Infiniband. So this may be a nice route to choose. JFj> This is not surprising as Gaussian is optimised to use very low networ= k JFj> bandwidth anyway. Our final decision was to invest in more memory and JFj> nodes! What about latency? Regards, Lev From owner-chemistry@ccl.net Wed Mar 17 18:16:00 2010 From: "Cyril Bauvais cyril.bauvais===bioquanta.net" To: CCL Subject: CCL: Hydrogen bond analysis Message-Id: <-41484-100317125823-19259-dq8wR5hbiEwikVWR5JEf2Q()server.ccl.net> X-Original-From: Cyril Bauvais Content-Type: multipart/alternative; boundary=001485f2756ce80ced0482020412 Date: Wed, 17 Mar 2010 17:58:10 +0100 MIME-Version: 1.0 Sent to CCL by: Cyril Bauvais [cyril.bauvais%bioquanta.net] --001485f2756ce80ced0482020412 Content-Type: text/plain; charset=ISO-8859-1 Hi, you can use ambertools (ptraj) or analyse tools from gromacs some scripts in VMD can do this also and for a single frame from trajectory, using pdb format, you can use ligplot Cyril 2010/3/16 Daniel Tunega daniel.tunega-.-univie.ac.at < owner-chemistry###ccl.net> > > Sent to CCL by: "Daniel Tunega" [daniel.tunega__univie.ac.at] > > > Hello all, > > can anybody recommend a program (preferentially open source) > doing a hydrogen bond analysis (e.g. average No. of H-bonds/molecule, etc.) > on MD/MC outputs (format of output file is not a key problem). > > Thanks, > Daniel> > > > --001485f2756ce80ced0482020412 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

you can use ambertools (ptraj) or analyse tools from gromacs
= some scripts in VMD can do this also
and for a single frame from traject= ory, using pdb format, you can use ligplot

Cyril

2010/3/16 Daniel Tunega daniel.tunega-.-uni= vie.ac.at <owner-chemistry###ccl.net>

Sent to CCL by: "Daniel =A0Tunega" [daniel.tunega__univie.ac.at]


Hello all,

can anybody recommend a program (preferentially open source)
doing a hydrogen bond analysis (e.g. average No. of H-bonds/molecule, etc.)=
on MD/MC outputs (format of output file is not a key problem).

Thanks,
Daniel



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--001485f2756ce80ced0482020412-- From owner-chemistry@ccl.net Wed Mar 17 19:49:00 2010 From: "Carlos Simmerling carlos.simmerling%%gmail.com" To: CCL Subject: CCL: ACS COMP Division Outstanding Junior Faculty Award- March 30 deadline Message-Id: <-41485-100317190727-13334-cj9X1MRkMVAZGFxIFBODbw-,-server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Wed, 17 Mar 2010 19:07:23 -0400 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling[a]gmail.com] The ACS COMP/HP Outstanding Junior Faculty Award program provides $1,000 to each of four outstanding tenure-track junior faculty members to present their work in COMP symposia at ACS National Meetings. The Awards are designed to assist new faculty members in gaining visibility within the COMP community. Award certificates and $1,000 prizes will be presented at the COMP Poster session. While special consideration will be given to Assistant Professors presenting work in the area of algorithm and methods development, applications for Outstanding Junior Faculty Awards are invited from all current tenure-track junior faculty who are members of ACS and the ACS Division of Computers in Chemistry. Postdoctoral researchers in transition to faculty appointments may also be considered. Selection criteria will include the novelty and importance of the work to be presented, CV of the applicant, as well as the level of Departmental support as indicated by the applicant's department Chair or Chair designee. To apply for an award for the ACS National Meeting in Boston, MA, August 22-26, 2010, an extended abstract of the work (no more than 2 pages), a CV and the letter of departmental support should be sent as pdf or text files to carlos.simmerling(!)gmail.com. Please include your last name and the type of information (CV, abstract, etc.) in the file name. The application deadline is 5pm on March 30. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by April 1, 2010, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal poster abstract to the " Outstanding Junior Faculty Award " symposium on the ACS PACS system prior to the PACS deadline. Note that you MUST APPLY TWICE: email your application, and submit an abstract to PACS. Both must be submitted before their respective deadlines. We also suggest that if desired, HP award applicants submit a separate abstract to PACS for an oral presentation in a relevant session, in addition to their poster abstract in the HP award section (note that acceptance into the oral sessions is not guaranteed). More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-632-1336 carlos.simmerling(!)gmail.com From owner-chemistry@ccl.net Wed Mar 17 20:24:00 2010 From: "Carlos Simmerling carlos.simmerling*|*gmail.com" To: CCL Subject: CCL: ACS COMP Division Graduate Award in Supercomputing- March 30 deadline Message-Id: <-41486-100317190355-9451-lFz5rIvY5Yc2UhtpVY6OjQ-*-server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Wed, 17 Mar 2010 19:03:51 -0400 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling~!~gmail.com] Two Graduate Student Awards in Supercomputing to be awarded at the Fall 2010 Boston ACS National Meeting The ACS Graduate Student Award in Supercomputing has been created to provide supercomputer resources to outstanding students in the early stages of their graduate career, particularly for projects that need high performance computing resources for their chemistry-related project. Those eligible for the award are graduate students in good standing who are carrying out research in the broadly defined area of computational chemistry. Winners (or their adviser, if necessary) will be the Principal Investigator of a new account on the kraken supercomputer at the National Institute of Computational Sciences (NICS). They will also be honored during a ceremony at the COMP Division poster session. Applicants are encouraged (but not required) to present work within the COMP program at the meeting, either in oral or poster format. The awardees are chosen on the basis of: the significance of the project plan, potential impact on the project of additional supercomputer resources, qualifications of the student, and the strength of the supporting letter and other materials. Application requirements for the ACS National Meeting in Boston include an extended abstract of the work (no more than 1 page), a two page CV, a brief letter of support from the research advisor, and a 1 page computational plan indicating: computational resources already available for the project, the types of calculations to be performed, availability of software, justification of number and length of runs, and an estimate of the total time needed (up to 200,000 CPU hours maximum). Please include your last name and the type of information (CV, abstract, etc.) in the file name. For information about kraken, see http://www.nics.tennessee.edu/computing-resources/kraken. There is a limit of one Supercomputing Award application per research lab (PI) per award type. These should be sent as pdf or text files (no other formats accepted) to carlos.simmerling*gmail.com. Please include your last name and the type of information (CV, abstract, etc.) in the file name. The application deadline is 5pm on March 30. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by April 1, 2010, please contact the organizer immediately by telephone (see below). If you want to present your work in an oral or poster presentation, you must also submit your abstract using the ACS PACS system, prior to the PACS deadline. More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-632-1336 carlos.simmerling*gmail.com From owner-chemistry@ccl.net Wed Mar 17 20:59:00 2010 From: "Fabian Boes fabian.boes ~~ certara.com" To: CCL Subject: CCL: Tripos webinar and European workshops Message-Id: <-41487-100317183151-19550-KPyxRTV0WtmWQ3tOyovltw*|*server.ccl.net> X-Original-From: "Fabian Boes" Date: Wed, 17 Mar 2010 18:31:47 -0400 Sent to CCL by: "Fabian Boes" [fabian.boes .. certara.com] Dear colleagues, You are cordially invited to attend the following events: "Use of Pharmacophore, Shape and Receptor Components in SYBYLs UNITY for Compound Virtual Screening" Webinar, Tuesday, 30 March 2010 11AM New York (8AM San Francisco, 4PM London, 5PM Paris) "Trends and new technologies for lead optimization and in silico drug design" European workshops, Paris, April 13, 2010 & Cambridge (UK) April 14, 2010 For further information, workshop agenda, and registration please take a look at http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=events Kind regards, Dr. Fabian Bs Application Scientist Tripos A Certara Company From owner-chemistry@ccl.net Wed Mar 17 21:33:00 2010 From: "Delwar Hossain hossaind2004++yahoo.com" To: CCL Subject: CCL:G: Flory interaction parameter estimation using G03 Message-Id: <-41488-100317191957-17665-V2kQgZIPXxkOc5ivzEB3lw:_:server.ccl.net> X-Original-From: Delwar Hossain Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 17 Mar 2010 15:19:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Delwar Hossain [hossaind2004]![yahoo.com] As Andreas explained it will not be so eassy to calculate the Flory-Huggins= interaction parameters by using Gaussian. To calculate the Flory-Huggins i= nteraction parameters you need to calculate the cohesive interaction energy= . To calcualter cohesive interaction energy you can use MD programm like LA= MMPS or Materials Studio (Accelrys). You can also look for free MD programm= . Alternaively you can calculate solubility parameter and then calculate Fl= ory-Huggins interaction parameter easily. =20 Hope it will help. Thanks, Delwar --- On Wed, 3/17/10, Andreas Klamt klamt_-_cosmologic.de wrote: > From: Andreas Klamt klamt_-_cosmologic.de > Subject: CCL:G: Flory interaction parameter estimation using G03 > To: "Hossain, Delwar " > Date: Wednesday, March 17, 2010, 8:41 AM >=20 > Sent to CCL by: Andreas Klamt [klamt_+_cosmologic.de] > Dear Andreea, >=20 > I am afraid that what you are describing here does not make > much sense. > The Flory or Flory-Huggins interaction parameters are > effective > interaction parameters in the bulk liquid phase. And what > you express as > E in the formulas should be a free energy, not an > interaction enthalpy. > They have little to do with the interaction energies, which > you get when > you optimize pairs of molecules. Such pair would just probe > some optimally strong interactions at a small portion of the > surface, but in a liquid the molecules are interacting > everywhere. >=20 > Some of our industrial customers are using our COSMO-RS > method/COSMOtherm program to calculate Flory-Huggins > parameters, making use of the chemical potentials of the two > compounds in the 2 liquid phases calculted by COSMOtherm. > Indeed, we also have developed a special tool (COSMOmeso) to > set up the required DFT/COSMO and COSMOtherm calculations. >=20 > Alternative methods might be force-field based MD or MC > simulations or ab-initio-MD (Car-Parrinello) simulations, > but they are not simple, and COSMO-RS usually is more > accurate (see the industrial fluid property simuation > challenge)than the force-field based simulations, and I > doubt that you will be able to afford the calculation times > required for abinitio MD. >=20 > If you are lucky and have an older version of G03 (check > for the > existance of the keyword COSMORS) then you can do the > required DFT/COSMO > calculations with G03. But you will need a COSMO-RS > program, e.g. our > COSMOtherm, to do the thermodynamic postprocessing. >=20 > Best regards >=20 > Andreas >=20 > Andreea Cristina Balaceanu abalaceanu*_*yahoo.com schrieb: > > Sent to CCL by: "Andreea Cristina Balaceanu" > [abalaceanu(-)yahoo.com] > > Hello,=20 > > I am a PhD student and I want to use the Gaussian 03 > program to estimate the Flory interaction parameter between > a copolymer and water. I know that the Flory interaction > parameter is given by: X=3D z/kT[E_12 - 1/2(E_11 + E_22), > where X is the Flory interaction parameter, z is the > coordination number, E_12 is the interaction energy between > monomer and water, E_11 is the interaction energy between > water molecules, and E_22 is the interaction energy between > monomers. > >=20 > > I now that you can calculate the interaction energy in > the Gaussian program by using E_interaction=3D E_AB,bAB - > E_A,bAB - E_B,bAB, where bAB refers to the basis set.=20 > > My questions are: > > Can I estimate the Flory interaction parameter in this > way? > > How exactly do I calculate E_AB? Do I just put a > monomer next to a water molecule and compute the minimal > potential energy? The water molecules interact with the > polymer by hydrogen bondings, so do I set the distance > between my monomer and the water molecule of the order of a > hydrogen bond? > >=20 > > Thank you very much in advance for your help. > >=20 > > Andreea Balaceanu.> > >=20 > >=20 > >=20 >=20 >=20 >=20 > -=3D This is automatically added to each message by the > mailing script =3D- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the ~~ sign. You > can also>=20 > E-mail to subscribers: CHEMISTRY~~ccl.net > or use: > =A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message >=20 > E-mail to administrators: CHEMISTRY-REQUEST~~ccl.net > or use > =A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message >=20 > Subscribe/Unsubscribe:=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.= shtml >=20>=20Conferences: http://server.ccl.net/chemistry= /announcements/conferences/ >=20>=20> =A0 =A0=A0=A0http://www.ccl.net/spammers.txt >=20>=20 >=20 > =0A=0A=0A From owner-chemistry@ccl.net Wed Mar 17 22:09:00 2010 From: "John McKelvey jmmckel[#]gmail.com" To: CCL Subject: CCL:G: Gaussun 03 multiple nodes Message-Id: <-41489-100317170910-26533-48W9KCwLwo8ihTM1VWrEAQ(~)server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Mar 2010 16:05:06 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel[]gmail.com] FYI, ORCA also runs parallel. It uses OPENMPI on both SMP and distributed. To run SMP on only adds PALx where x=3D2..n processors, and it's free to academics. Haven't tried distributed. Very fast for big basis set Hartree-Fock and hybrid DFT runs. Joh McKelvey On Wed, Mar 17, 2010 at 11:21 AM, Jason Swails jason.swails---gmail.com wrote: > > Sent to CCL by: Jason Swails [jason.swails!A!gmail.com] > On Wed, Mar 17, 2010 at 3:15 AM, Peter Khlyabich khlyabic]^[usc.edu > wrote: >> >> Sent to CCL by: "Peter =A0Khlyabich" [khlyabic%%usc.edu] >> Dear colleagues, >> >> I'm trying to run Gaussian 03 E01. on multiple nodes. Unfortunately I fa= ced problems. When I run 1 node and 8 processors the calculations are done = without problems. As soon as the number of nodes is increased to 2 and more= I have problem with communication between the nodes as I suppose. > > Gaussian parallel engine is LINDA, which is strictly shared memory > parallelization. =A0Thus, it should only run on a single node (multiple > nodes would be operating in a distributed memory parallel environment > as opposed to shared memory). =A0I believe that NWChem and (maybe?) > QChem operate using MPI and distributed memory. > > Good luck! > Jason > > -- > --------------------------------------- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > > > > - 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> > > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel%x%gmail.com From owner-chemistry@ccl.net Wed Mar 17 22:43:00 2010 From: "MQO.Carlos Javier Nunez Aguero carlosjavierna(a)gmail.com" To: CCL Subject: CCL: Hydrogen bond analysis Message-Id: <-41490-100317210655-28804-q9T5DuWlKz+n4+JMrthcYg_._server.ccl.net> X-Original-From: "MQO.Carlos Javier Nunez Aguero" Content-Type: multipart/alternative; boundary=001485f20c5e7855670482086c77 Date: Wed, 17 Mar 2010 18:36:37 -0600 MIME-Version: 1.0 Sent to CCL by: "MQO.Carlos Javier Nunez Aguero" [carlosjavierna^gmail.com] --001485f20c5e7855670482086c77 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all You can use gOpenMol. http://www.csc.fi/english/pages/g0penMol With this software you can obtain a nice view o you can monitor the separation between two atoms along e.g. 4500 ps of simulation. gOpenMol can't save the results however. Have funny analysis, Carlos Javier El 17 de marzo de 2010 10:58, Cyril Bauvais cyril.bauvais=3D=3D=3Dbioquanta= .net < owner-chemistry%x%ccl.net> escribi=F3: > Hi, > > you can use ambertools (ptraj) or analyse tools from gromacs > some scripts in VMD can do this also > and for a single frame from trajectory, using pdb format, you can use > ligplot > > Cyril > > 2010/3/16 Daniel Tunega daniel.tunega-.-univie.ac.at < > owner-chemistry-$-ccl.net> > >> >> Sent to CCL by: "Daniel Tunega" [daniel.tunega__univie.ac.at] >> >> >> Hello all, >> >> can anybody recommend a program (preferentially open source) >> doing a hydrogen bond analysis (e.g. average No. of H-bonds/molecule, >> etc.) >> on MD/MC outputs (format of output file is not a key problem). >> >> Thanks, >> Daniel >> >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY-$-ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or use>> >> >> >> > --001485f20c5e7855670482086c77 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all

You can use gOpenMol.

http://www.csc.fi/englis= h/pages/g0penMol

With this software you can ob= tain a nice view o you can monitor the separation=A0
between two atoms=A0along e.g. 4500 ps of simulation.
gOpenM= ol can't save the results however.


<= div>Have funny analysis,
Carlos Javier






El 17 de marzo de 2010 10:58, Cyril Bauvais cyril.bauvais= =3D=3D=3Dbioquanta.net <owner-chemistry%x%ccl.net> escribi=F3:
Hi,

you can use ambertools (ptraj) o= r analyse tools from gromacs
some scripts in VMD can do this also
and= for a single frame from trajectory, using pdb format, you can use ligplot<= br>
Cyril

2010/3/16 Daniel Tunega daniel.tunega-.-univie.ac.at <owner-chemistry-$-ccl.net>=

Sent to CCL by: "Daniel =A0Tunega" [daniel.tunega__univie.ac.at]


Hello all,

can anybody recommend a program (preferentially open source)
doing a hydrogen bond analysis (e.g. average No. of H-bonds/molecule, etc.)=
on MD/MC outputs (format of output file is not a key problem).

Thanks,
Daniel




-=3D This is automatically added to each message by the mailing script =3D-
E-mail to subscribers: CHEMISTRY-$-ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

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=


--001485f20c5e7855670482086c77-- From owner-chemistry@ccl.net Wed Mar 17 23:18:00 2010 From: "Carlos Simmerling carlos.simmerling++gmail.com" To: CCL Subject: CCL: ACS COMP Division Graduate Student Awards- March 30 deadline Message-Id: <-41491-100317190126-7977-qJrEoFBxocpog82paPG/BQ.@.server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Wed, 17 Mar 2010 19:01:22 -0400 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling-$-gmail.com] Five $1,150 CCG Excellence Student Travel Award Stipends Available for the Fall 2010 Boston ACS National Meeting The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. The awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas (North, South or Central) are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. There is a limit of one CCG award application per research lab (PI). To apply for an award for the ACS National Meeting in Boston, MA, August 22-26, 2010, an extended abstract of the work (no more than 2 pages), a two page CV along with a letter of support from the research advisor, and a personal statement (no more than 1 page) should be sent as pdf or text files to carlos.simmerling|-|gmail.com. Please include your last name and the type of information (CV, abstract, etc.) in the file name. The application deadline is 5pm on March 30. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by April 1, 2010, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal poster abstract to the "Chemical Computing Group Excellence Award" symposium on the ACS PACS system prior to the PACS deadline. Note that you MUST APPLY TWICE: email your application, and submit an abstract to PACS. Both must be submitted before their respective deadlines. More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-632-1336 carlos.simmerling|-|gmail.com