From owner-chemistry@ccl.net Wed Mar 31 00:38:01 2010 From: "Jan Labanowski jkl---wowway.biz" To: CCL Subject: CCL: Avisto: A free workflow/project management system Message-Id: <-41555-100331003454-1368-qnFGuHQYivgPpzzCA9hPVQ%%server.ccl.net> X-Original-From: Jan Labanowski Content-Type: multipart/alternative; boundary="----=_Part_11991_1343957073.1270007821143" Date: Tue, 30 Mar 2010 23:57:01 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [jkl.-*-.wowway.biz] ------=_Part_11991_1343957073.1270007821143 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Dear CCL, Before you jump to conclusions, I was not paid for this. I simply think that this is good stuff.. Avisto is the first cloud-computing enabled software platform that enables connections of different molecular modeling tools into workflows and management of data in a transparent manner. And Avisto is FREE. Avisto platform supports applications from the Astonis Application Catalog, similar to Apple app store. Currently, the catalog has a growing list of molecular modeling tools, many are free and some are for sale. Promotion : For a limited time, new register users will receive: 1. 5 CPU hours for Basic QChem tool (sufficient for two years of undergraduate general and organic chemistry courses). 2. 5 CPU hours for Mopac GUI Cloud (sufficient for running hundred of moderate size molecules using the MOPAC2009 Program. 3. 6-month free license for using Mopac GUI Pro for running the MOPAC2009 program on your local computers. Avisto is an excellent tool for teaching chemistry. A number of exercises in General, Organic, Inorganic, and Physical Chemistry are also available. You can download Avisto at http://www.astonis.com and start your experiment with computational chemistry. http://md01.wow.synacor.com/service/home/~/image001.jpg?auth=co&loc=en_US&id=5061&part=3 Jan Labanowski jkl-*-ccl.net ------=_Part_11991_1343957073.1270007821143 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit

Dear CCL,

Before you jump to conclusions, I was not paid for this. I simply think that this is good stuff..

Avisto is the first cloud-computing enabled software platform that enables connections of different molecular modeling tools into workflows and management of data in a transparent manner. And Avisto is FREE.

Avisto platform supports applications from the Astonis Application Catalog, similar to Apple app store. Currently, the catalog has a growing list of molecular modeling tools, many are free and some are for sale.

Promotion: For a limited time, new register users will receive:

5 CPU hours for Basic QChem tool (sufficient for two years of undergraduate general and organic chemistry courses).
5 CPU hours for Mopac GUI Cloud (sufficient for running hundred of moderate size molecules using the MOPAC2009 Program.
6-month free license for using Mopac GUI Pro for running the MOPAC2009 program on your local computers.

Avisto is an excellent tool for teaching chemistry. A number of exercises in General, Organic, Inorganic, and Physical Chemistry are also available.

You can download Avisto at http://www.astonis.com and start your experiment with computational chemistry.

Jan Labanowski

jkl-*-ccl.net

------=_Part_11991_1343957073.1270007821143-- From owner-chemistry@ccl.net Wed Mar 31 04:22:01 2010 From: "Vincent Leroux vincent.leroux_+_loria.fr" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41556-100330191417-20682-GLcPSipGKx7OypmaUPsMYQ:_:server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 31 Mar 2010 00:24:42 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr] Hi, I have one question. When will the 3D vision drivers be available under Linux? Thanks in advance VL Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a écrit : > Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] > Dear CCL community, > > We are happy to announce that several molecular dynamics and quantum chemistry software are now available on GPUs. These are listed at: > http://www.nvidia.com/object/tesla_bio_workbench.html > > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, GROMOS, > HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX protein-protein > docking software is available too. > > Some of these like ABINIT, GROMOS, and HEX are still not linked from the link > above but can be found at: > ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L_Sim/BigDFT/ > GROMOS http://code.google.com/p/gpugromos/ > HEX http://www.loria.fr/~ritchied/hex/ > > Please feel free to contact me if you have questions. > > Regards > Sumit > sumitg AT nvidia com > > > From owner-chemistry@ccl.net Wed Mar 31 09:00:00 2010 From: "andras.borosy-.-givaudan.com" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41557-100331055810-3368-6KbbKG065RsW1lMxhy2UxQ_._server.ccl.net> X-Original-From: andras.borosy:-:givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0033AF3BC12576F7_=" Date: Wed, 31 Mar 2010 11:24:32 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy ~ givaudan.com This is a multipart message in MIME format. --=_alternative 0033AF3BC12576F7_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Sumit, Is there a QC application available at this hardware which is able to=20 generate COSMO-files? http://www.cosmologic.de/index.php?cosId=3D1700&crId=3D1 Best wishes, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Sumit Gupta sugupta^-^nvidia.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com###ccl.net 30.03.2010 19:57 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Announce: Several MD / QC codes available for GPUs Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] Dear CCL community, We are happy to announce that several molecular dynamics and quantum=20 chemistry software are now available on GPUs. These are listed at: http://www.nvidia.com/object/tesla=5Fbio=5Fworkbench.html The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS,=20 GROMOS,=20 HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX protein-protein = docking software is available too. Some of these like ABINIT, GROMOS, and HEX are still not linked from the=20 link=20 above but can be found at: ABINIT http://www.abinit.org/ uses BigDFT=20 http://inac.cea.fr/L=5FSim/BigDFT/ GROMOS http://code.google.com/p/gpugromos/ HEX http://www.loria.fr/~ritchied/hex/ Please feel free to contact me if you have questions. Regards Sumit sumitg AT nvidia com -=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 0033AF3BC12576F7_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Sumit,

Is there a QC application available at this hardware which is able to generate COSMO-files?

http://www.cosmologic.de/index.php?c= osId=3D1700&crId=3D1

Best wishes,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf - Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http:= //www.givaudan.com

"Sumit Gupta sug= upta^-^nvidia.com" <owner-chemistry###ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com###ccl.net

30.03.2010 19:57

Please respond to
"CCL Subscribers" <chemistry###ccl.net>

To	"Borosy, Andras " <andras.borosy###givaudan.com>
cc
Subject	CCL: Announce: Several MD / QC codes available for GPUs

Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] Dear CCL community, We are happy to announce that several molecular dynamics and quantum chemis= try software are now available on GPUs. These are listed at: http://www.nvidia.com/object/tesla=5Fbio=5Fworkbench.html The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, GROMOS, HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX protein-pro= tein docking software is available too. Some of these like ABINIT, GROMOS, and HEX are still not linked from the link above but can be found at: ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L=5FSim/= BigDFT/ GROMOS http://code.google.com/p/gpugromos/ HEX http://www.loria.fr/~ritchied/hex/ Please feel free to contact me if you have questions. Regards Sumit sumitg AT nvidia com -=3D This is automatically added to each message by the mailing script =3D-= http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage http://www.ccl.net/chemistry/sub=5Funsub.shtml http://www.ccl.net/spammers.txt
--=_alternative 0033AF3BC12576F7_=-- From owner-chemistry@ccl.net Wed Mar 31 09:35:01 2010 From: "Iain Moal Iain.Moal##cancer.org.uk" To: CCL Subject: CCL: any software to draw schlegel diagrams of water clusters? Message-Id: <-41558-100331070817-31199-mM9BWj56CIJMr3me6G8X1A!A!server.ccl.net> X-Original-From: "Iain Moal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CAD0B9.CA9BD32B" Date: Wed, 31 Mar 2010 11:04:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Iain Moal" [Iain.Moal(_)cancer.org.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01CAD0B9.CA9BD32B Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You can do this wither either Pymol or VMD. Both allow you to set the poi= nt of view and have orthographic options. -----Original Message----- > From: owner-chemistry+iain.moal=3D=3Dcancer.org.uk]*[ccl.net on behalf of Ra= j Thakur rajthakuor=3D-=3Dgmail.com Sent: Sun 28/03/2010 18:35 To: Iain Moal Subject: CCL: any software to draw schlegel diagrams of water clusters? =20 Dear Sir/madam, Can you please tell me which graphical software can be use= d to draw schlegel diagram of dodecahedron water cluster. Best regards, raj This communication is from Cancer Research UK. Our website is at www.cance= rresearchuk.org. We are a charity registered under number 1089464 and a co= mpany limited by guarantee registered in England & Wales under number 4325= 234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. O= ur central telephone number is 020 7242 0200. =20 This communication and any attachments contain information which is confid= ential and may also be privileged. It is for the exclusive use of the in= tended recipient(s). If you are not the intended recipient(s) please note= that any form of disclosure, distribution, copying or use of this communi= cation or the information in it or in any attachments is strictly prohibit= ed and may be unlawful. If you have received this communication in error,= please notify the sender and delete the email and destroy any copies of i= t. =20 E-mail communications cannot be guaranteed to be secure or error free, as = information could be intercepted, corrupted, amended, lost, destroyed, arr= ive late or incomplete, or contain viruses. We do not accept liability fo= r any such matters or their consequences. Anyone who communicates with us= by e-mail is taken to accept the risks in doing so. ------_=_NextPart_001_01CAD0B9.CA9BD32B-- From owner-chemistry@ccl.net Wed Mar 31 10:10:00 2010 From: "raj f thakuor rajthakuor .. gmail.com" To: CCL Subject: CCL: schlegel diagram Message-Id: <-41559-100330061745-32304-KCVdPvWNKxrzHwq8SOACIw++server.ccl.net> X-Original-From: "raj f thakuor" Date: Tue, 30 Mar 2010 06:17:44 -0400 Sent to CCL by: "raj f thakuor" [rajthakuor##gmail.com] Dear Sir/madam, Can you please tell me which graphical software can be used to draw schlegel diagram of dodecahedron water cluster. Best regards, raj From owner-chemistry@ccl.net Wed Mar 31 10:53:00 2010 From: "Anton Nizovtsev nanto[A]mail.ru" To: CCL Subject: CCL:G: Oscillator strength Message-Id: <-41560-100331105044-7870-KIOz1CjwtzHKBtg7Z07rEw^-^server.ccl.net> X-Original-From: "Anton Nizovtsev" Date: Wed, 31 Mar 2010 10:50:35 -0400 Sent to CCL by: "Anton Nizovtsev" [nanto-$-mail.ru] Thank you for response! I am interesting in singlet-singlet transition from A(S0)B(S0) to A*(T1)B*(T1). This case seems to be not trivial. The question is to calculate oscillator strength of such transition. Id like to know your opinion about applicability of linear response methods (namely, TDDFT, CCn etc.) and other possible methods to my problem. Thanks in advance Anton > "Alexander Bagaturyants bagaturyants%x%gmail.com" wrote: > > Sent to CCL by: "Alexander Bagaturyants" [bagaturyants a gmail.com] > Dear Anton, > The answer depends on what you mean under "simultaneous S0-T1 transitions of > each molecular fragment". If you consider that the transition in the complex > must be a linear combination of states like A*(T1)B(S0) + A(S0)B*(T1) or A*B > - AB*, this is one thing; to calculate such a state, you should just > consider your complex in the same way as an isolated component. I believe > that the transition energy in the complex will be almost the same as in the > isolated component, and the two states (A*B + AB* or A*B - AB*) will be near > degenerate. The state will have the T1 symmetry. However, if you is > interested in the state that corresponds to the simultaneous S0-T1 > transition in both components, you must consider the state A*(T1)B*(T1), > which is somewhat more complicated. First, the energy of this state must be > about twice as large as the energy of the transition in the isolated > component. So you must consider many excited states in order to locate the > desired energy range. Next, you will get three different spin states (again, > near degenerate) for such a configuration, singlet, triplet, and quintet. > You may use any available QC program, like free GAMESS, Orca, etc., or > commercial Gaussian, Turbomole, etc. > Happy calculations > Best regards, > > Prof. Alexander A. Bagatur'yants > Photochemistry Center > Russian Academy of Sciences > ul. Novatorov 7a > Moscow 119421 Russia > Phone: +7(495)9362588 (office) > +7(916)5317022 (mobile) > Fax: +7(495)9361255 > e-mail: sasha],[photonics.ru > bagaturyants],[gmail.com > > > -----Original Message----- > > From: owner-chemistry+sasha==photonics.ru],[ccl.net > [mailto:owner-chemistry+sasha==photonics.ru],[ccl.net] On Behalf Of Anton > Nizovtsev nanto#,#mail.ru > Sent: Monday, March 29, 2010 2:47 PM > To: Bagaturyants, Alexander A. > Subject: CCL: Oscillator strength > > > Sent to CCL by: "Anton Nizovtsev" [nanto^-^mail.ru] > > Suppose there are two molecules in its singlet ground states separated at > several angstroms (5, for example). I want to calculate excitation energy > and oscillator strength for transition between ground state of such complex > and excited state corresponding simultaneous S0-T1 transitions of each > molecular fragment. Is it possible to perform? Which methods are suitable > for this problem in quantum chemical programs? > > Thanks in advance > Anton > > nanto],[mail.ruhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > From owner-chemistry@ccl.net Wed Mar 31 14:15:01 2010 From: "Sumit Gupta sugupta_._nvidia.com" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41561-100331141204-28969-LlVmcsOIAH5Q0wDNKujL+Q!=!server.ccl.net> X-Original-From: Sumit Gupta Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 31 Mar 2010 09:51:39 -0700 MIME-Version: 1.0 Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com] Linux drivers for 3D Vision are already available: http://www.nvidia.com/object/linux_display_amd64_195.36.15.html You will need a GPU board with the stereo connector and we currently only= =20support the Samsung and Viewsonic panels. Since this topic is of limited interest to the rest of the CCL community,= can you please send me a note to my nvidia email address. Sumit -----Original Message----- > From: owner-chemistry+sugupta=3D=3Dnvidia.com**ccl.net [mailto:owner-chemi= stry+sugupta=3D=3Dnvidia.com**ccl.net] On Behalf Of Vincent Leroux vincent= .leroux_+_loria.fr Sent: Tuesday, March 30, 2010 15:25 To: Sumit Gupta Subject: CCL: Announce: Several MD / QC codes available for GPUs Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr] Hi, I have one question. When will the 3D vision drivers be available under Linux? Thanks in advance VL Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a =E9crit : > Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] > Dear CCL community, >=20 > We are happy to announce that several molecular dynamics and quantum ch= emistry software are now available on GPUs. These are listed at: > http://www.nvidia.com/object/tesla_bio_workbench.html >=20 > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, = GROMOS,=20 > HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX protein-prot= ein=20 > docking software is available too. >=20 > Some of these like ABINIT, GROMOS, and HEX are still not linked from th= e link=20 > above but can be found at: > ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L_Sim/Big= DFT/ > GROMOS http://code.google.com/p/gpugromos/ > HEX http://www.loria.fr/~ritchied/hex/ >=20 > Please feel free to contact me if you have questions. >=20 > Regards > Sumit > sumitg AT nvidia com >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D= -=20=20Subscribe/Unsubscribe:=20 =20Job: http://www.ccl.net/jobs=20=20-------------------------------------------------------------------------= ---------- This email message is for the sole use of the intended recipient(s) and m= ay contain confidential information. Any unauthorized review, use, disclosure or di= stribution is prohibited. If you are not the intended recipient, please contact the= =20sender by reply email and destroy all copies of the original message. -------------------------------------------------------------------------= ---------- From owner-chemistry@ccl.net Wed Mar 31 14:51:00 2010 From: "Carlos F. Lagos cflagos-,-uc.cl" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41562-100331123152-13335-h3+8LACW4f12LiGw3m5arA-$-server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 31 Mar 2010 12:54:55 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [cflagos#,#uc.cl] Is Autodock also available as free code?=20 -----Mensaje original----- De: owner-chemistry+carlos=3D=3Dcbuc.cl**ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl**ccl.net] En nombre de = Vincent Leroux vincent.leroux_+_loria.fr Enviado el: Martes, 30 de Marzo de 2010 19:25 Para: Lagos, Carlos F Asunto: CCL: Announce: Several MD / QC codes available for GPUs Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr] Hi, I have one question. When will the 3D vision drivers be available under Linux? Thanks in advance VL Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a =E9crit : > Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] > Dear CCL community, >=20 > We are happy to announce that several molecular dynamics and quantum chemistry software are now available on GPUs. These are listed at: > http://www.nvidia.com/object/tesla_bio_workbench.html >=20 > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, GROMOS,=20 > HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX = protein-protein > docking software is available too. >=20 > Some of these like ABINIT, GROMOS, and HEX are still not linked from = the link=20 > above but can be found at: > ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L_Sim/BigDFT/ > GROMOS http://code.google.com/p/gpugromos/ > HEX http://www.loria.fr/~ritchied/hex/ >=20 > Please feel free to contact me if you have questions. >=20 > Regards > Sumit > sumitg AT nvidia com >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt__________ Informaci=F3n de ESET NOD32 Antivirus, versi=F3n de la base = de firmas de virus 4987 (20100331) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 __________ Informaci=F3n de ESET NOD32 Antivirus, versi=F3n de la base = de firmas de virus 4987 (20100331) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 From owner-chemistry@ccl.net Wed Mar 31 15:26:01 2010 From: "EDMUND.NDIP/a\HAMPTONU.EDU" To: CCL Subject: CCL: Avisto: A free workflow/project management system Message-Id: <-41563-100331105729-13376-TETc0Zhl+ZDJeYPTyxbngw|*|server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CAD0DC.C8AA38F1" Date: Wed, 31 Mar 2010 10:12:10 -0400 MIME-Version: 1.0 Sent to CCL by: [EDMUND.NDIP**HAMPTONU.EDU] This is a multi-part message in MIME format. ------_=_NextPart_001_01CAD0DC.C8AA38F1 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Thanks Jan. I concur. I have it on all the machines in my office. I am u= sing it in my P. Chem class. I'll try it out on a small research problem. Edmund Moses N. Ndip, PhD Chemistry Department School of Science Hampton University Hampton, VA 23668 -----Original Message----- > From: owner-chemistry+edmund.ndip=3D=3Dhamptonu.edu(_)ccl.net on behalf of Ja= n Labanowski jkl---wowway.biz Sent: Tue 3/30/2010 11:57 PM To: NDIP EDMUND Subject: CCL: Avisto: A free workflow/project management system =20 Dear CCL,=20 Before you jump to conclusions, I was not paid for this. I simply think tha= t this is good stuff..=20 Avisto is the first cloud-computing enabled software platform that enables = connections of different molecular modeling tools into workflows and manage= ment of data in a transparent manner. And Avisto is FREE.=20 Avisto platform supports applications from the Astonis Application Catalog,= similar to Apple app store. Currently, the catalog has a growing list of m= olecular modeling tools, many are free and some are for sale.=20 Promotion : For a limited time, new register users will receive:=20 1. 5 CPU hours for Basic QChem tool (sufficient for two years of underg= raduate general and organic chemistry courses).=20 2. 5 CPU hours for Mopac GUI Cloud (sufficient for running hundred of m= oderate size molecules using the MOPAC2009 Program.=20 3. 6-month free license for using Mopac GUI Pro for running the MOPAC20= 09 program on your local computers.=20 Avisto is an excellent tool for teaching chemistry. A number of exercises i= n General, Organic, Inorganic, and Physical Chemistry are also available.= =20 You can download Avisto at http://www.astonis.com and start your experiment= with computational chemistry.=20 http://md01.wow.synacor.com/service/home/~/image001.jpg?auth=3Dco&loc=3Den_= US&id=3D5061&part=3D3 Jan Labanowski=20 jkl * ccl.net=20 The information contained in this message is intended only for the recipien= t, and may otherwise be privileged and confidential. If the reader of this = message is not the intended recipient, or an employee or agent responsible = for delivering this message to the intended recipient, please be aware that= any dissemination or copying of this communication is strictly prohibited.= If you have received this communication in error, please immediately notif= y us by replying to the message and deleting it from your computer. This fo= otnote also confirms that this email has been scanned for all viruses by th= e Hampton University Center for Information Technology Enterprise Systems s= ervice. ------_=_NextPart_001_01CAD0DC.C8AA38F1-- From owner-chemistry@ccl.net Wed Mar 31 17:25:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom]~[gmail.com" To: CCL Subject: CCL: Oscillator strength Message-Id: <-41564-100331140358-21739-x+qlvR4iHXLAHxW+hDs8HA%x%server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 31 Mar 2010 19:10:20 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom:gmail.com] On Wed, Mar 31, 2010 at 4:50 PM, Anton Nizovtsev nanto[A]mail.ru wrote: > > Sent to CCL by: "Anton =A0Nizovtsev" [nanto-$-mail.ru] > Thank you for response! > I am interesting in singlet-singlet transition from A(S0)B(S0) to A*(T1)B= *(T1). This case seems to be not trivial. The question is to calculate osci= llator strength of such transition. Id like to know your opinion about appl= icability of linear response methods (namely, TDDFT, CCn etc.) and other po= ssible methods to my problem. Since this is a double excitation I think you will have trouble with TDDFT. In principle it sounds like something that would be suitable for perturbation theory (i.e. compute the T1 states separately and couple them afterwards), but I don't immediately know of a program that can do this. Best bet seems to be a CI with a suitably defined state space, but your result may depend strongly on this space. I think Molcas can compute overlap between two configurations defined > from different sets of orbitals, which is what you get if you do a separate state optimization. Maybe linear response SOPPA (available in Dalton) can do it, but then you have to carefully identify the right state. I was trying to think of some approximation where you compute, say, A*(T1)B(S0) as an unrestricted ground state, and do tddft from there, but didn't come up with anything useful. Regards, Ulf Ekstrom, VU University Amsterdam From owner-chemistry@ccl.net Wed Mar 31 18:00:01 2010 From: "Sumit Gupta sugupta]~[nvidia.com" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41565-100331154511-13009-qjY9DWTj4Oo28uXrBihlZg:+:server.ccl.net> X-Original-From: Sumit Gupta Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 31 Mar 2010 12:44:58 -0700 MIME-Version: 1.0 Sent to CCL by: Sumit Gupta [sugupta:nvidia.com] There is an early partial port of AutoDock: http://sourceforge.net/projects/gpuautodock/ There is one more effort to port AutoDock from HCL Infosystems (they are looking for customers interested in this port). Earlier work on AutoDock has shown a healthy speedup http://www.siliconinformatics.com/products.html But this company is no longer marketing AutoDock. There are also efforts to port Dock as well (again looking for potential users). A Japanese group (Akiyama et al) out of Tokyo Tech has ported=20 MegaDock protein-to-protein docking to CUDA. http://research.microsoft.com/en-us/events/ersymposium2009/accelerated_cl= usters_proteomics_2.pdf Sumit ---- Sumit Gupta Sr. Manager - Tesla GPU HPC Group NVIDIA -----Original Message----- > From: owner-chemistry+sugupta=3D=3Dnvidia.com]![ccl.net [mailto:owner-chemi= stry+sugupta=3D=3Dnvidia.com]![ccl.net] On Behalf Of Carlos F. Lagos cflago= s-,-uc.cl Sent: Wednesday, March 31, 2010 08:55 To: Sumit Gupta Subject: CCL: Announce: Several MD / QC codes available for GPUs Sent to CCL by: "Carlos F. Lagos" [cflagos#,#uc.cl] Is Autodock also available as free code?=20 -----Mensaje original----- De: owner-chemistry+carlos=3D=3Dcbuc.cl_._ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl_._ccl.net] En nombre de Vince= nt Leroux vincent.leroux_+_loria.fr Enviado el: Martes, 30 de Marzo de 2010 19:25 Para: Lagos, Carlos F=20 Asunto: CCL: Announce: Several MD / QC codes available for GPUs Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr] Hi, I have one question. When will the 3D vision drivers be available under Linux? Thanks in advance VL Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a =E9crit : > Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] > Dear CCL community, >=20 > We are happy to announce that several molecular dynamics and quantum chemistry software are now available on GPUs. These are listed at: > http://www.nvidia.com/object/tesla_bio_workbench.html >=20 > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, GROMOS,=20 > HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX protein-prot= ein > docking software is available too. >=20 > Some of these like ABINIT, GROMOS, and HEX are still not linked from th= e link=20 > above but can be found at: > ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L_Sim/BigDFT/ > GROMOS http://code.google.com/p/gpugromos/ > HEX http://www.loria.fr/~ritchied/hex/ >=20 > Please feel free to contact me if you have questions. >=20 > Regards > Sumit > sumitg AT nvidia com >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/cgi-bin/ccl/send_ccl_messageJo= b: http://www.ccl.net/jobs__________ Info= rmaci=F3n de ESET NOD32 Antivirus, versi=F3n de la base de firmas de virus 4987 (20100331) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 __________ Informaci=F3n de ESET NOD32 Antivirus, versi=F3n de la base de= =20firmas de virus 4987 (20100331) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 -=3Dis is automatically added to each message by the mailing script =3D=20=20Subscribe/Unsubscribe:=20 =20Job: http://www.ccl.net/jobs=20=20-------------------------------------------------------------------------= ---------- This email message is for the sole use of the intended recipient(s) and m= ay contain confidential information. Any unauthorized review, use, disclosure or di= stribution is prohibited. If you are not the intended recipient, please contact the= =20sender by reply email and destroy all copies of the original message. -------------------------------------------------------------------------= ---------- From owner-chemistry@ccl.net Wed Mar 31 20:40:00 2010 From: "Igor Filippov Contr igorf],[helix.nih.gov" To: CCL Subject: CCL: Announce: Several MD / QC codes available for GPUs Message-Id: <-41566-100331173317-5641-IjGPtZdnRh5hn9Pq31LHhA|,|server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 31 Mar 2010 16:59:18 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf(~)helix.nih.gov] I'm interested in 3D stereo as well. Could you tell us (off-list or on-list) what monitors/glasses nvidia recommends for 3d stereo? Igor On Wed, 2010-03-31 at 12:51 -0400, Sumit Gupta sugupta_._nvidia.com wrote: > Sent to CCL by: Sumit Gupta [sugupta .. nvidia.com] > Linux drivers for 3D Vision are already available: > http://www.nvidia.com/object/linux_display_amd64_195.36.15.html > > You will need a GPU board with the stereo connector and we currently only support the Samsung and Viewsonic panels. > > Since this topic is of limited interest to the rest of the CCL community, > can you please send me a note to my nvidia email address. > > Sumit > > -----Original Message----- > > From: owner-chemistry+sugupta==nvidia.com.:.ccl.net [mailto:owner-chemistry+sugupta==nvidia.com.:.ccl.net] On Behalf Of Vincent Leroux vincent.leroux_+_loria.fr > Sent: Tuesday, March 30, 2010 15:25 > To: Sumit Gupta > Subject: CCL: Announce: Several MD / QC codes available for GPUs > > > Sent to CCL by: Vincent Leroux [vincent.leroux||loria.fr] > Hi, > > I have one question. > > When will the 3D vision drivers be available under Linux? > > Thanks in advance > VL > > > > Le 30/03/10 19:57, Sumit Gupta sugupta^-^nvidia.com a Ã©crit : > > Sent to CCL by: "Sumit Gupta" [sugupta/a\nvidia.com] > > Dear CCL community, > > > > We are happy to announce that several molecular dynamics and quantum chemistry software are now available on GPUs. These are listed at: > > http://www.nvidia.com/object/tesla_bio_workbench.html > > > > The software includes AMBER, ABINIT (based on BigDFT), ACEMD, GROMACS, GROMOS, > > HOOMD, LAMMPS, NAMD, TeraChem, VMD. For docking, the HEX protein-protein > > docking software is available too. > > > > Some of these like ABINIT, GROMOS, and HEX are still not linked from the link > > above but can be found at: > > ABINIT http://www.abinit.org/ uses BigDFT http://inac.cea.fr/L_Sim/BigDFT/ > > GROMOS http://code.google.com/p/gpugromos/ > > HEX http://www.loria.fr/~ritchied/hex/ > > > > Please feel free to contact me if you have questions. > > > > Regards > > Sumit > > sumitg AT nvidia com----------------------------------------------------------------------------------- > This email message is for the sole use of the intended recipient(s) and may contain > confidential information. Any unauthorized review, use, disclosure or distribution > is prohibited. If you are not the intended recipient, please contact the sender by > reply email and destroy all copies of the original message. > ----------------------------------------------------------------------------------- > > > > -=is is automatically added to each message by the mailing script => > From owner-chemistry@ccl.net Wed Mar 31 21:40:00 2010 From: "Jamin Krinsky jamink_-_berkeley.edu" To: CCL Subject: CCL:G: TD-DFT opt failing in G09 Message-Id: <-41567-100331202858-32664-djHQ9ISeOlAZ8QJvKJTNnQ*server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 31 Mar 2010 16:58:35 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink(~)berkeley.edu] Dear forum, I have a user who is getting a mysterious failure message while attempting TD-DFT optimizations in G09. It's related to link 914 but it doesn't make sense. Here is the route section: #p opt td=(singlets,nstates=6,root=1) rb3lyp/6-31+g(d) nosymm int=ultrafine scf(xqc,maxconventionalcycles=60) The calculation runs for 6 geometry steps but the first excited state energy is quite oscillatory. At the 7th step, it quits with the following error: No map to state 1 You need to solve for more vectors in order to follow this state. Error termination via Lnk1e in /usr/software/gaussian/g09.revA02/l914.exe If he's following the 1st excited state then he shouldn't need more states (increasing "nstates" to 20 does not help). I've never seen this although my experience with this algorithm is minimal, and although that error has come up a couple of times in these threads I haven't seen a conclusive explanation. Any help with this would be appreciated. Regards, Jamin -- 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