From owner-chemistry@ccl.net Mon Feb 9 06:29:01 2009 From: "Michel Petitjean petitjean.chiral]-[gmail.com" To: CCL Subject: CCL: Release of DIVCF and MCG freewares Message-Id: <-38578-090209062127-21581-RqaXVAH7qzpJaWbBFc/Wrg###server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=0015175770b25f0c2f04627a9127 Date: Mon, 9 Feb 2009 12:21:11 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral|-|gmail.com] --0015175770b25f0c2f04627a9127 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCLers, I am very pleased to announce you the release of two freewares: DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers. Download: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF DIVCF reads the N sets of cartesian coordinates of the molecule, then computes the (N*N) array of minimized RMS distances between them. This array of non euclidean distances is submitted to a hierarchical ascending classification with the MCG (Modified Clustering Gain) as the stop criterion, which gives K clusters of conformers. The K mean points of the clusters are the K retained conformers. MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed. Download: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#MCG MCG reads, either an (N*N) array of distances or dissimilarities, or an array containing N lines (individuals) and P columns (numerical variables), which will be converted into an (N*N) array of euclidean distances. Then MCG computes an optimal partition. The f77 subroutine source performing the ascending hierarchical clustering with stop criterion is provided (it is commented in french, but should be understandable from the theory). Reference for both freewares: J.E. Meslamani, F. Andre, M. Petitjean; J. Chem. Inf. Model. 2009 (DOI: 10.1021/ci800275k) All my best, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean|*|cea.fr, petitjean.chiral|*|gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html --0015175770b25f0c2f04627a9127 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLers,

I am very pleased to announce you the release of two fr= eewares:


DIVCF: Selects by clustering major conformations of a m= olecule in a set of its conformers.
Download: http://petitjeanmiche= l.free.fr/itoweb.petitjean.freeware.html#DIVCF

DIVCF reads the N sets of cartesian coordinates of the molecule,
the= n computes the (N*N) array of minimized RMS distances between them.
This= array of non euclidean distances is submitted to a hierarchical
ascendi= ng classification with the MCG (Modified Clustering Gain)
as the stop criterion, which gives K clusters of conformers.
The K mean = points of the clusters are the K retained conformers.


MCG: Optim= al Partition (classification): numerical variables and non-euclidean spaces= .
The number of classes is computed.
Download: http://petitjeanmichel.f= ree.fr/itoweb.petitjean.freeware.html#MCG

MCG reads, either an (= N*N) array of distances or dissimilarities,
or an array containing N lines (individuals) and P columns
(numerical va= riables), which will be converted into an
(N*N) array of euclidean dista= nces.
Then MCG computes an optimal partition.

The f77 subroutine = source performing the ascending hierarchical clustering with stop criterion=
is provided (it is commented in french, but should be understandable from t= he theory).


Reference for both freewares:
J.E. Meslamani, F. = Andre, M. Petitjean; J. Chem. Inf. Model. 2009 (DOI: 10.1021/ci800275k)


All my best,

Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS U= RA 2096), CEA Saclay, bat. 528,
91191 Gif-sur-Yvette Cedex, France.
P= hone: +331 6908 4006 / Fax: +331 6908 4007
E-mail: michel.petitjean|*|cea.fr, petitjean.chiral|*|gmail.com
http= ://petitjeanmichel.free.fr/itoweb.petitjean.shape.html

--0015175770b25f0c2f04627a9127-- From owner-chemistry@ccl.net Mon Feb 9 08:55:00 2009 From: "William Huang b95203004:_:ntu.edu.tw" To: CCL Subject: CCL: NPT and NVT simulations Message-Id: <-38579-090209035045-16109-amBZuDHNuvcRrpdRNoUf0Q^^server.ccl.net> X-Original-From: "William Huang" Date: Mon, 9 Feb 2009 03:50:41 -0500 Sent to CCL by: "William Huang" [b95203004^ntu.edu.tw] Hi all, I am using TINKER 4.2 to simulate an infinite long amyloid fibrils, under periodic box condition, and SASA solvation model (continuum solvation), I have two possible methods: 1. minimization --> NPT --> NPV 2. minimization --> NPT my fellow worker in the lab suggested the first one, however, I am curious about the validity of the second method, it would be nice if anyone can asnwer me. Thanks From owner-chemistry@ccl.net Mon Feb 9 09:31:00 2009 From: "Rosa Amanda Weber rosa.weber%scienomics.com" To: CCL Subject: CCL: The Scienomics Scientific Forum Message-Id: <-38580-090209055847-9686-mj8JHQVcTn/Wa/0d9T2G6A * server.ccl.net> X-Original-From: "Rosa Amanda Weber" Date: Mon, 9 Feb 2009 05:58:43 -0500 Sent to CCL by: "Rosa Amanda Weber" [rosa.weber]^[scienomics.com] Scienomics invites you to join the Scienomics scientific forum SciForum online at www.scienomics.com/SciForum. Since 2004 Scienomics develops scientific software for industrial partners as well as academic and governmental institutes in Materials research and today Scienomics has launched a forum to encourage communication and discussion of the latest research in Materials simulations and to offer academia and industry a high-ranking platform for the exchange of knowledge on an international scale. Who can use the SciForum? SciForum is a private service for MAPS users, as well as scientist. (Registered users are welcome to use their existing login data when prompted for login information, if you are not registered, please register to be able to post messages). A few reasons why you should use SciForum We will actively use the SciForum discussions as a means of extending our knowledge base for your benefit. You will have the opportunity to share your experience with other MAPS users. Updates, patches, Bugs and fixes for example can be posted and discussed openly. Cordially, Rosa Weber rosa.weber^^scienomics.com From owner-chemistry@ccl.net Mon Feb 9 10:06:00 2009 From: "Pavle Mocilac pavle.mocilac2(!)mail.dcu.ie" To: CCL Subject: CCL:G: Error in energy computation procedure Message-Id: <-38581-090208105924-13682-aoybm8YKoraG/1IlD8zxMA=-=server.ccl.net> X-Original-From: "Pavle Mocilac" Date: Sun, 8 Feb 2009 10:59:20 -0500 Sent to CCL by: "Pavle Mocilac" [pavle.mocilac2 : mail.dcu.ie] Hi I am new to this list and new to Gaussian 03 software as well so probably my problem will be trivial to you. There are two things I am concerned: 1. Energy calculations of small molecules in crystal form: I got CIF file from crystallographic survey and now I want to calculate total energy of a molecule in crystal, together with all intramolecular and intermolecular bonds and contacts that make the crystal cell unit stable. The method I was advised is to upload original CIF file with whole crystal cell unit and periodic interactions and to make a job file (B3LYP/6-311++G, %mem=80MW, k-Space Integration Method = default), and to start the calculation. The obtained total energy should be divided with 4 since there are 4 molecules in cell unit and that value would represent energy of the molecule in crystal form. Is this a right way to do that? Is there something to be set using Crystal Editor? 2. Immediate Error! I managed to make such a job file, started the calculation but the G03 crushed shortly with an error: dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 66048 FType=2 FMxFil=10000 Number 0 Base 20480 End 66048 End1 66048 Wr Pntr 20480 Rd Pntr 20480 Length 45568 Error termination in NtrErr: NtrErr Called from FileIO. Whats going on there? Is there anything to be adjusted during the job preparations? Is there any one having experience with calculations of crystals? Thanks in advance! Pavle Mocilac PhD Student Dublin City Univerity From owner-chemistry@ccl.net Mon Feb 9 12:58:01 2009 From: "aa aa**chemaxon.hu" To: CCL Subject: CCL: First call for papers: ChemAxon's 2009 European UGM and Training Day, June 3-4 and June 2, Budapest, Hungary Message-Id: <-38582-090209125500-12538-xbItW1+VDHdwJx0tg2R2Lg|-|server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------010109080308080007080907" Date: Mon, 09 Feb 2009 18:54:47 +0100 MIME-Version: 1.0 Sent to CCL by: aa [aa{}chemaxon.hu] This is a multi-part message in MIME format. --------------010109080308080007080907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excuse cross postings Good day, ChemAxon's 2009 European User Group Meeting will be held on Wednesday and Thursday, June 3-4th at the Danubius Resort on Margit Island, Budapest, Hungary. The meeting will preceded by a training day on June 2nd. The User Group Meeting will feature oral and poster presentations from ChemAxon users, scientists, developers and partners as well as our usual range of social events to mix, speak and enjoy with staff and peers. We are inviting those interested in presenting at the meeting to submit abstracts for review. The deadline for receipt of oral abstracts is March 27th. To find out more and submit your abstract please visit: http://www.chemaxon.com/UGM/07/index.html. The presentations archive, including previous meeting reports from Wendy Warr and Yvonne Martin, is here: http://www.chemaxon.com/UGM/ugm_land.html. The Developer Workshop and End User Training day on June 2nd (2 tracks) will give hands on experience with ChemAxon functionality and best practices, for topics see : http://www.chemaxon.com/training/UGM0609.html We hope you can join us for what has proven to be a most interesting and enjoyable cheminformatics event. See you there. Alex Alex Allardyce Marketing Dir. ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce --------------010109080308080007080907 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Excuse cross postings

Good day,

ChemAxon's 2009 European User Group Meeting will be held on Wednesday and Thursday, June 3-4th at the Danubius Resort on Margit Island, Budapest, Hungary. The meeting will preceded by a training day on June 2nd.

The User Group Meeting will feature oral and poster presentations > from ChemAxon users, scientists, developers and partners as well as our usual range of social events to mix, speak and enjoy with staff and peers.

We are inviting those interested in presenting at the meeting to submit abstracts for review. The deadline for receipt of oral abstracts is March 27th. To find out more and submit your abstract please visit: http://www.chemaxon.com/UGM/07/index.html. The presentations archive, including previous meeting reports from Wendy Warr and Yvonne Martin, is here: http://www.chemaxon.com/UGM/ugm_land.html.

The Developer Workshop and End User Training day on June 2nd (2 tracks) will give hands on experience with ChemAxon functionality and best practices, for topics see : http://www.chemaxon.com/training/UGM0609.html
We hope you can join us for what has proven to be a most interesting and enjoyable cheminformatics event.

See you there.

Alex

Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435

--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce
--------------010109080308080007080907-- From owner-chemistry@ccl.net Mon Feb 9 15:32:01 2009 From: "=?ISO-2022-JP?B?GyRCJDckThsoQg==?= quarashino ~~ gmail.com" To: CCL Subject: CCL: ADF: excited-state optimization Message-Id: <-38583-090209100018-10269-7s2glx0U4MVwqZfrWI7/Aw+/-server.ccl.net> X-Original-From: =?ISO-2022-JP?B?GyRCJDckThsoQg==?= Content-Type: multipart/alternative; boundary=001636e90cdd10fece04627da034 Date: Mon, 9 Feb 2009 10:00:02 -0500 MIME-Version: 1.0 Sent to CCL by: =?ISO-2022-JP?B?GyRCJDckThsoQg==?= [quarashino---gmail.com] --001636e90cdd10fece04627da034 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All, How can one do excited-state geometry optimizations in ADF? Thanks in advance, Shino --001636e90cdd10fece04627da034 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All,

How can one do excited-state geometry optimizations in ADF?

Thanks in advance,

Shino --001636e90cdd10fece04627da034-- From owner-chemistry@ccl.net Mon Feb 9 16:10:00 2009 From: "Joy Ku joyku^_^stanford.edu" To: CCL Subject: CCL: New release of OpenMM enables molecular dynamics acceleration on GPUs Message-Id: <-38584-090209153352-20070-ht0dyurEnJR2VyPJHQunJw,server.ccl.net> X-Original-From: "Joy Ku" Date: Mon, 9 Feb 2009 15:33:48 -0500 Sent to CCL by: "Joy Ku" [joyku%stanford.edu] OpenMM is a freely downloadable, high performance, extensible library that allows molecular dynamics (MD) simulations to run on high performance computer architectures, such as graphics processing units (GPUs). Significant performance speed ups of over 100X were achieved in some cases using OpenMM. The current release includes a version of GROMACS that integrates the OpenMM library, enabling it to be sped up on high-end NVIDIA and AMD/ATI graphics boards. OpenMM can be downloaded from http://simtk.org/home/openmm. OpenMM Zephyr, an easy-to-use application for MD that uses GROMACS-OpenMM, is available from http://simtk.org/home/zephyr. Read the full press release here: http://news-service.stanford.edu/pr/2009/pr-molecmorel-021109.html ______________________________________________________ Joy P. Ku, PhD Director of Dissemination Simbios, Stanford University (W) 650.736.8434 (F) 650.723.7461 Email: joyku*stanford.edu Website: http://simbios.stanford.edu From owner-chemistry@ccl.net Mon Feb 9 20:29:00 2009 From: "aditya chhikara adichhikara:gmail.com" To: CCL Subject: CCL: question about viewing homo energies in molpro Message-Id: <-38585-090209202741-12430-C0Vm9+15bPTuy9HbyStPPg{}server.ccl.net> X-Original-From: "aditya chhikara" Date: Mon, 9 Feb 2009 20:27:37 -0500 Sent to CCL by: "aditya chhikara" [adichhikara-*-gmail.com] Hello, I had a question about viewing HOMO energies in Molpro. How does one get Molpro to printout HOMO energies in the output? Cheers, Adi From owner-chemistry@ccl.net Mon Feb 9 21:40:00 2009 From: "Zork Zou zorkzou*gmail.com" To: CCL Subject: CCL: ADF: excited-state optimization Message-Id: <-38586-090209213751-9490-x3mP5+jP8Fd5l0jGtHKbAA++server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=000e0cd4d8e6cee8a30462875e58 Date: Mon, 9 Feb 2009 20:37:37 -0600 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou%%gmail.com] --000e0cd4d8e6cee8a30462875e58 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You can use the keywords OCCUPATIONS or UNRESTRICTED + CHARGE for individua= l states. A more general method is TDDFT. TDDFT geometry optimization (by analytical or numerical gradient) may be not supported by the present version of ADF, but can be carried out numerically with OPTIM or MINI utility programs through a user's interface. http://web.uniovi.es/qcg/optim.html http://pagesperso.lcp.u-psud.fr/lauvergnat/mini/mini.html On Mon, Feb 9, 2009 at 9:00 AM, =E3=81=97=E3=81=AE quarashino ~~ gmail.com = < owner-chemistry#ccl.net> wrote: > Dear All, > > How can one do excited-state geometry optimizations in ADF? > > Thanks in advance, > > Shino --000e0cd4d8e6cee8a30462875e58 Content-Type: text/html; charset=ISO-2022-JP Content-Transfer-Encoding: base64 PGRpdj4KPHAgY2xhc3M9Ik1zb05vcm1hbCIgc3R5bGU9Ik1BUkdJTjogMGNtIDBjbSAwcHQiPjxz cGFuIGxhbmc9IkVOLVVTIj48Zm9udCBmYWNlPSJUaW1lcyBOZXcgUm9tYW4iIHNpemU9IjMiPllv dSBjYW4gdXNlIHRoZSBrZXl3b3JkcyZuYnNwO09DQ1VQQVRJT05TIG9yIFVOUkVTVFJJQ1RFRCAr IENIQVJHRSBmb3IgaW5kaXZpZHVhbCBzdGF0ZXMuIEEgbW9yZSBnZW5lcmFsIG1ldGhvZCBpcyBU RERGVC4gVERERlQgZ2VvbWV0cnkgb3B0aW1pemF0aW9uIChieSBhbmFseXRpY2FsIG9yIG51bWVy aWNhbCBncmFkaWVudCkgbWF5IGJlIG5vdCBzdXBwb3J0ZWQgYnkgdGhlIHByZXNlbnQgdmVyc2lv biBvZiBBREYsIGJ1dCBjYW4gYmUgY2FycmllZCBvdXQgbnVtZXJpY2FsbHkgd2l0aCBPUFRJTSBv ciBNSU5JIHV0aWxpdHkgcHJvZ3JhbXMgdGhyb3VnaCBhIHVzZXIncyBpbnRlcmZhY2UuPC9mb250 Pjwvc3Bhbj48L3A+Cgo8cCBjbGFzcz0iTXNvTm9ybWFsIiBzdHlsZT0iTUFSR0lOOiAwY20gMGNt IDBwdCI+PHNwYW4gbGFuZz0iRU4tVVMiPjxmb250IGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgc2l6 ZT0iMyI+PC9mb250Pjwvc3Bhbj4mbmJzcDs8L3A+CjxwIGNsYXNzPSJNc29Ob3JtYWwiIHN0eWxl PSJNQVJHSU46IDBjbSAwY20gMHB0Ij48c3BhbiBsYW5nPSJFTi1VUyI+PGZvbnQgZmFjZT0iVGlt ZXMgTmV3IFJvbWFuIiBzaXplPSIzIj48YSBocmVmPSJodHRwOi8vd2ViLnVuaW92aS5lcy9xY2cv b3B0aW0uaHRtbCI+aHR0cDovL3dlYi51bmlvdmkuZXMvcWNnL29wdGltLmh0bWw8L2E+PC9mb250 Pjwvc3Bhbj48L3A+CjxwIGNsYXNzPSJNc29Ob3JtYWwiIHN0eWxlPSJNQVJHSU46IDBjbSAwY20g MHB0Ij48c3BhbiBsYW5nPSJFTi1VUyI+PGZvbnQgZmFjZT0iVGltZXMgTmV3IFJvbWFuIiBzaXpl PSIzIj48YSBocmVmPSJodHRwOi8vcGFnZXNwZXJzby5sY3AudS1wc3VkLmZyL2xhdXZlcmduYXQv bWluaS9taW5pLmh0bWwiPmh0dHA6Ly9wYWdlc3BlcnNvLmxjcC51LXBzdWQuZnIvbGF1dmVyZ25h dC9taW5pL21pbmkuaHRtbDwvYT48L2ZvbnQ+PC9zcGFuPjwvcD4KPC9kaXY+CjxkaXY+Jm5ic3A7 PC9kaXY+CjxkaXY+T24gTW9uLCBGZWIgOSwgMjAwOSBhdCA5OjAwIEFNLCAbJEIkNyROGyhCIHF1 YXJhc2hpbm8gfn4gPGEgaHJlZj0iaHR0cDovL2dtYWlsLmNvbSI+Z21haWwuY29tPC9hPiA8c3Bh biBkaXI9Imx0ciI+Jmx0OzxhIGhyZWY9Im1haWx0bzpvd25lci1jaGVtaXN0cnlAY2NsLm5ldCI+ b3duZXItY2hlbWlzdHJ5QGNjbC5uZXQ8L2E+Jmd0Ozwvc3Bhbj4gd3JvdGU6PGJyPjwvZGl2Pgo8 ZGl2IGNsYXNzPSJnbWFpbF9xdW90ZSI+CjxibG9ja3F1b3RlIGNsYXNzPSJnbWFpbF9xdW90ZSIg c3R5bGU9IlBBRERJTkctTEVGVDogMWV4OyBNQVJHSU46IDBweCAwcHggMHB4IDAuOGV4OyBCT1JE RVItTEVGVDogI2NjYyAxcHggc29saWQiPkRlYXIgQWxsLDxicj48YnI+SG93IGNhbiBvbmUgZG8g ZXhjaXRlZC1zdGF0ZSBnZW9tZXRyeSBvcHRpbWl6YXRpb25zIGluIEFERj88YnI+PGJyPlRoYW5r cyBpbiBhZHZhbmNlLDxicj4KPGJyPlNoaW5vIDwvYmxvY2txdW90ZT48L2Rpdj48YnI+Cg== --000e0cd4d8e6cee8a30462875e58--