On = Sep 17, 2012, at 7:13 PM, Tain Rodrigues Costa = tainaliscano=3D-=3Dglobomail.com wrote:

Sent to CCL by: "Tain   Rodrigues = Costa" [tainaliscano[-]globomail.com]
Dear researches,

I am = doing some semi-empirical calculations with the PM7 method.
I am = running frequency calculations. I would like to know if there is any = progam to visualize the frequency of the molecules.

Thanks in = advance,

Tain Rodrigues,
Undergraduate studant of farmacy of = Universidade Federal Fluminense (UFF)

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= --Apple-Mail-1468-278573349-- From owner-chemistry@ccl.net Tue Sep 18 04:52:00 2012 From: "meishway linkon meishwaylinkon~~yahoo.com" To: CCL Subject: CCL: Error: segmentation violation Message-Id: <-47613-120918045106-3734-XhnLrIz5BOnUbDiDgpvA2g|*|server.ccl.net> X-Original-From: "meishway linkon" Date: Tue, 18 Sep 2012 04:51:05 -0400 Sent to CCL by: "meishway linkon" [meishwaylinkon()yahoo.com] hello everyone ! I have completed crystal state prediction calculations for my x shape compound for determination of coupling integral , after prediction calculation i ran geometry optimization with forcite field,using compass26 , charge using gate gasteiger in the material studio for lowest energy 5 structures (structure with space group P-1 was lowest energy structure ). but after measuring neighboring pathways , when i run a monomer file for with this route sectionin in gaussin over linux : # pw91pw91/6-31G(?d)punch mo-nosymm but it is ending with following error : Error: segmentation violation rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff rdx 0000000000007932, rsp 00007fff46c419e8, rbp 00007fff46c41fc0 rsi 000000000000000b, rdi 0000000000007932, r8 00002ab49dd104e0 r9 0000000000000000, r10 0000000000000000, r11 0000000000000206 r12 0000000000000000, r13 0000000000000000, r14 00007fff46c42008 r15 00002ab49dd11050 0 0x30ff2306f7 1 0x510155 lnk1e_ + 0x225 2 0x4f3c00 gauerr_ + 0x80 3 0x410fdd uhfopn_ + 0xd8ad 4 0x403710 MAIN_ + 0xb0 5 0x403648 real 84m44.028s user 503m21.417s sys 4m28.084s what should i do please suggest me ? From owner-chemistry@ccl.net Tue Sep 18 05:26:00 2012 From: "Arthur Zalevsky aozalevsky-*-gmail.com" To: CCL Subject: CCL: Mopac output file visualizer Message-Id: <-47614-120918044612-3518-uYbbINyfkHbuVuB4TN8kjg:+:server.ccl.net> X-Original-From: Arthur Zalevsky Content-Type: multipart/alternative; boundary=f46d043be0b6ba06d304c9f5ebad Date: Tue, 18 Sep 2012 12:46:05 +0400 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky(~)gmail.com] --f46d043be0b6ba06d304c9f5ebad Content-Type: text/plain; charset=UTF-8 You can try gabedit: http://gabedit.sourceforge.net/ It's either free and opensource. 2012/9/17 Tain Rodrigues Costa tainaliscano=-=globomail.com < owner-chemistry[#]ccl.net> > > Sent to CCL by: "Tain Rodrigues Costa" [tainaliscano[-]globomail.com] > Dear researches, > > I am doing some semi-empirical calculations with the PM7 method. > I am running frequency calculations. I would like to know if there is any > progam to visualize the frequency of the molecules. > > Thanks in advance, > > Tain Rodrigues, > Undergraduate studant of farmacy of Universidade Federal Fluminense (UFF)> > > --f46d043be0b6ba06d304c9f5ebad Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable You can try gabedit:=C2=A0http:= //gabedit.sourceforge.net/

It's either free and opensource.

2012/9/17 Tain Rodrigues Costa tainal= iscano=3D-=3Dglobomail.com <o= wner-chemistry[#]ccl.net>

Sent to CCL by: "Tain =C2=A0 Rodrigues Costa" [tainaliscano[-]globomail.com]
Dear researches,

I am doing some semi-empirical calculations with the PM7 method.
I am running frequency calculations. I would like to know if there is any p= rogam to visualize the frequency of the molecules.

Thanks in advance,

Tain Rodrigues,
Undergraduate studant of farmacy of Universidade Federal Fluminense (UFF)

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--f46d043be0b6ba06d304c9f5ebad-- From owner-chemistry@ccl.net Tue Sep 18 06:02:00 2012 From: "John Keller jwkeller=alaska.edu" To: CCL Subject: CCL: Mopac output file visualizer Message-Id: <-47615-120918045352-4531-8iaFO7EhnfK6uSQkHaYeWQ- -server.ccl.net> X-Original-From: John Keller Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 18 Sep 2012 00:53:45 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller#alaska.edu] Hi Tain, You can upload mopac output.out files (or log files from several programs) at the WebMO website www.webmo.net. Log on as guest. I just uploaded one (calculated locally here) "Pyridine-Freq-Mopac". You can use the vibration animation, symmetry element graphics, MO or ESP graphics too. John Keller Department of Chemistry and Biochemistry University of Alaska Fairbanks On Mon, Sep 17, 2012 at 9:13 AM, Tain Rodrigues Costa tainaliscano=-=globomail.com wrote: > > Sent to CCL by: "Tain Rodrigues Costa" [tainaliscano[-]globomail.com] > Dear researches, > > I am doing some semi-empirical calculations with the PM7 method. > I am running frequency calculations. I would like to know if there is any progam to visualize the frequency of the molecules. > > Thanks in advance, > > Tain Rodrigues, > Undergraduate studant of farmacy of Universidade Federal Fluminense (UFF)> > From owner-chemistry@ccl.net Tue Sep 18 07:19:00 2012 From: "Ramon Crehuet rcsqtc]_[iqac.csic.es" To: CCL Subject: CCL: Propagation of photon Message-Id: <-47616-120918070535-30359-zIuSdQWqMccC5JEmyzdy8g _ server.ccl.net> X-Original-From: "Ramon Crehuet" Date: Tue, 18 Sep 2012 07:05:34 -0400 Sent to CCL by: "Ramon Crehuet" [rcsqtc#%#iqac.csic.es] Hi Sergio, I apologize for such a late answer. This is an old book, but it deals with relativistic Schroedinger equation and the interaction of matter and radiation. "Advanced Molecular Quantum Mechanics: An Introduction to Relativistic Quantum Mechanics and the Quantum Theory of Radiation" by R. E. Moss (1973) Best regards, Ramon From owner-chemistry@ccl.net Tue Sep 18 08:44:00 2012 From: "Gkourmpis, Thomas Thomas.Gkourmpis,borealisgroup.com" To: CCL Subject: CCL: Looking for MD program to model droplets Message-Id: <-47617-120918035350-16702-v8h6GpsYiuSSHwf9IwvNZQ^server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 18 Sep 2012 09:53:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis*borealisgroup.com] Peeter Hi There are a number of really capable MD software packages available that can be parallelised and offer a wide range of capabilities. If you are looking for open licence software LAMMPS or NAMD are pretty good and able to handle large number of atoms. LAMMPS doesn't have a full pre/post processing GUI so you will need to arrange for one. One option is MAPS from a company called Scienomics that offers these capabilities. NAMD has a GUI (it is called VMD) but MAPS can also be used to setup and analyse jobs without too much trouble. If you want to get a fully commercial package (MD code and GUI integrated together) then probably check what Accelrys offers, as they have a wide range of software packages for specific applications. Here are the relevant web pages for you to check what is most appropriate for your needs LAMMPS http://lammps.sandia.gov/ NAMD http://www.ks.uiuc.edu/Research/namd/ VMD http://www.ks.uiuc.edu/Research/vmd/ Scienomics http://scienomics.com/ Accelrys http://accelrys.com/ I hope this helps but if you need any more help/information give us a shout Thomas Dr Thomas Gkourmpis Researcher - Innovation & Technology Borealis AB | SE-444 86 Stenungsund | Sweden Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 www.borealisgroup.com | 556078-6633 | Swedish Companies Registration Office ___________________________________ Borealis - Shaping the Future with Plastics -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com..ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com..ccl.net] On Behalf Of Peeter Burk peeter|a|chem.ut.ee Sent: Tuesday, September 18, 2012 8:15 AM To: Gkourmpis, Thomas Subject: CCL: Looking for MD program to model droplets Sent to CCL by: "Peeter Burk" [peeter#,#chem.ut.ee] Dear colleagues, We are planning to extend our activities to the MD modeling of droplets in atmosphere. Could anyone suggest a suitable program, which can be used for MD modeling of water and also other solvent (e.g. acetonitrile, DMSO) droplets containing some organic solutes (neutral and also cationic or anionic forms). The program should be capable of handling droplet of several thousand molecules in a reasonable time. So far we have had some preliminary tries with tinker and amoeba force field with some success, but tinker seems not to be parallelized so I would like to inquire about other (faster, better, etc.) options. Best regards Peeter Burk University of Tartu, Estonia burk{=}ut.eehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Tue Sep 18 09:19:00 2012 From: "Ramon Crehuet rcsqtc(_)iqac.csic.es" To: CCL Subject: CCL: Propagation of photon Message-Id: <-47618-120918060737-4943-kV+a7wlTQwQj6ExW2YdOMw|-|server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=UTF-8 Date: Tue, 18 Sep 2012 12:07:51 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc-#-iqac.csic.es]

Hi Sergio,
I apologize for such a late answer.
This is an old book, but it deals with relativistic Schroedinger equation and the interaction of matter and radiation.
"Advanced Molecular Quantum Mechanics: An Introduction to Relativistic Quantum Mechanics and the Quantum Theory of Radiation" by R. E. Moss (1973)
Best regards,
Ramon

On 09/09/12 13:39, Sergio Manzetti sergio.manzetti/agmx.com wrote:

Dear CCLers, does anyone have an idea on a mathematical concept or proof that shows how electromagnetism can alternate a photons energy? I am working on a proof, but I am not able to link the Schrödinger equation of a photon to electromagnetism, neither in a particle or in a wave-state. Thus, is there a proof of concept where electrogmatisms is able to affect the energy of the wave-component of a photon?

Best wishes

Sergio

-- 
**************************************************************
Ramon Crehuet, PhD
Tenured researcher (Cientific titular)
Institute of Advanced Chemistry of Catalunya
http://www.iqac.csic.es/qteor
https://twitter.com/rcrehuet
IQAC - CSIC
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain)
**************************************************************

From owner-chemistry@ccl.net Tue Sep 18 09:54:00 2012 From: "Ramon Crehuet rcsqtc,iqac.csic.es" To: CCL Subject: CCL: Propagation of photon Message-Id: <-47619-120918061212-8480-EYqXH5q29MT+r7VVkf+EGQ^^^server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Tue, 18 Sep 2012 12:12:26 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc!A!iqac.csic.es] Hi Sergio, I apologize for such a late answer. This is an old book, but it deals with relativistic Schroedinger equation and the interaction of matter and radiation. "Advanced Molecular Quantum Mechanics: An Introduction to Relativistic Quantum Mechanics and the Quantum Theory of Radiation" by R. E. Moss (1973) Best regards, Ramon On 09/09/12 13:39, Sergio Manzetti sergio.manzetti/agmx.com wrote: > Dear CCLers, does anyone have an idea on a mathematical concept or proof that > shows how electromagnetism can alternate a photons energy? I am working on a > proof, but I am not able to link the Schrödinger equation of a photon to > electromagnetism, neither in a particle or in a wave-state. Thus, is there a > proof of concept where electrogmatisms is able to affect the energy of the > wave-component of a photon? > > Best wishes > > Sergio -- ************************************************************** Ramon Crehuet, PhD Tenured researcher (Cientific titular) Institute of Advanced Chemistry of Catalunya http://www.iqac.csic.es/qteor https://twitter.com/rcrehuet IQAC - CSIC Tel. +34 934006116 Jordi Girona 18-26 08034 Barcelona (Spain) ************************************************************** From owner-chemistry@ccl.net Tue Sep 18 10:47:01 2012 From: "Jussi Lehtola jussi.lehtola^^^helsinki.fi" To: CCL Subject: CCL: Looking for MD program to model droplets Message-Id: <-47620-120918042628-31124-2Hv3/C18EXt/SK4uSNeBIQ[]server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 18 Sep 2012 11:26:19 +0300 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola#%#helsinki.fi] On Tue, 18 Sep 2012 02:14:49 -0400 "Peeter Burk peeter|a|chem.ut.ee" wrote: > > Sent to CCL by: "Peeter Burk" [peeter#,#chem.ut.ee] > Dear colleagues, > > We are planning to extend our activities to the MD modeling of > droplets in atmosphere. Could anyone suggest a suitable program, > which can be used for MD modeling of water and also other solvent > (e.g. acetonitrile, DMSO) droplets containing some organic solutes > (neutral and also cationic or anionic forms). The program should be > capable of handling droplet of several thousand molecules in a > reasonable time. So far we have had some preliminary tries with > tinker and amoeba force field with some success, but tinker seems not > to be parallelized so I would like to inquire about other (faster, > better, etc.) options. GROMACS? It's parallellized and one of the fastest programs out there. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola:+:helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola:+:helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Tue Sep 18 12:45:00 2012 From: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer jerome.kieffer|-|terre-adelie.org" To: CCL Subject: CCL:G: Error: segmentation violation Message-Id: <-47621-120918123732-7610-Y4sdxCil1+cgq6e7NzKvqw-$-server.ccl.net> X-Original-From: =?ISO-8859-1?Q?J=E9r=F4me?= Kieffer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 18 Sep 2012 18:37:21 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?J=E9r=F4me?= Kieffer [jerome.kieffer|a|terre-adelie.org] On Tue, 18 Sep 2012 04:51:05 -0400 "meishway linkon meishwaylinkon~~yahoo.com" wrote: > what should i do please suggest me ? Contact Accelerys' support (if you are using their interface). Have you checked charges and total spin in gaussian input? Cheers, -- J�r�me Kieffer From owner-chemistry@ccl.net Tue Sep 18 14:39:00 2012 From: "carlos franca carfranca120(-)gmail.com" To: CCL Subject: CCL: Mopac output file visualizer Message-Id: <-47622-120918143000-30913-rd8ELvMq2lQkuN0FHuevVQ~~server.ccl.net> X-Original-From: carlos franca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Sep 2012 15:29:22 -0300 MIME-Version: 1.0 Sent to CCL by: carlos franca [carfranca120() gmail.com] hi rodrigues costa you can visualize normal modes of vibrational calculations with avogadro software http://avogadro.openmolecules.net/wiki/Main_Page El 17/09/12 14:13, Tain Rodrigues Costa tainaliscano=-=globomail.com escribi�: > Sent to CCL by: "Tain Rodrigues Costa" [tainaliscano[-]globomail.com] > Dear researches, > > I am doing some semi-empirical calculations with the PM7 method. > I am running frequency calculations. I would like to know if there is any progam to visualize the frequency of the molecules. > > Thanks in advance, > > Tain Rodrigues, > Undergraduate studant of farmacy of Universidade Federal Fluminense (UFF)> > >