From owner-chemistry@ccl.net Tue Oct 15 06:45:00 2013 From: "Scott Mckechnie jsm78|cam.ac.uk" To: CCL Subject: CCL: Accurate vertical ionization energies Message-Id: <-49239-131015064307-26410-0liNHFWZWizZ2h0eC3Biwg(!)server.ccl.net> X-Original-From: "Scott Mckechnie" Date: Tue, 15 Oct 2013 06:43:06 -0400 Sent to CCL by: "Scott Mckechnie" [jsm78 a cam.ac.uk] Dear all, I would like to compare vertical ionization energies obtained from DFT with highly accurate energies computed from a higher level method. I was hoping to get a sense of the accuracy of DFT ionization energies from different functionals and basis sets. I've noticed CCSD(T) is commonly used and I'm wondering what people would recommend. Also, any references would be much appreciated. Best wishes, Scott From owner-chemistry@ccl.net Tue Oct 15 07:19:00 2013 From: "Paolo Nicolini niko_pd]^[yahoo.it" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49240-131015041427-14100-Q2Hvg6vQ/DFCf0HZFAN3nQ*server.ccl.net> X-Original-From: Paolo Nicolini Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 15 Oct 2013 10:15:00 +0200 MIME-Version: 1.0 Sent to CCL by: Paolo Nicolini [niko_pd{=}yahoo.it] Dear Franois, the quick way to monitor a dihedral angle, in my opinion, is with VMD. You simply load your trajectory file, select the 4 atoms from mouse>label, and then you will find the time profile of the dihedral in graphics>labels>dihedrals. You can download VMD here: http://www.ks.uiuc.edu/Research/vmd/ It is for free for academics after registration. Best regards, Paolo ------------------------------------------ Paolo Nicolini, PhD Department of Control Engineering - K335 Faculty of Electrical Engineering Czech Technical University in Prague On 10/14/2013 08:17 PM, Elaine Meng meng. . .cgl.ucsf.edu wrote: > Sent to CCL by: "Elaine Meng" [meng**cgl.ucsf.edu] > Hi Francois, > There are probably many solutions, and perhaps a nongraphical one would be most efficient... however, depending on your trajectory file formats, you may be able to display the trajectory in Chimera, plot various various measurements (including dihedrals) versus frame, and "dump values" from the plots into text files. > > The Chimera tool is "MD Movie," see documentation including "Startup and Input" and "Plotting": > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html > > Chimera is free to download (Mac, Windows, Linux) for any noncommercial use. > http://www.rbvi.ucsf.edu/chimera/index.html > > Best, > 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 Tue Oct 15 07:54:00 2013 From: "Paolo Nicolini niko_pd**yahoo.it" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49241-131015044425-16677-NOMRagMlHv97xt5EuExcvQ{:}server.ccl.net> X-Original-From: Paolo Nicolini Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 15 Oct 2013 10:44:58 +0200 MIME-Version: 1.0 Sent to CCL by: Paolo Nicolini [niko_pd:-:yahoo.it] Dear Franois, the quick way to monitor a dihedral angle, in my opinion, is with VMD. You simply load your trajectory file, select the 4 atoms from mouse>label, and then you will find the time profile of the dihedral in graphics>labels>dihedrals. You can download VMD here: http://www.ks.uiuc.edu/Research/vmd/ It is for free for academics after registration. Best regards, Paolo ------------------------------------------ Paolo Nicolini, PhD Department of Control Engineering - K335 Faculty of Electrical Engineering Czech Technical University in Prague On 10/14/2013 07:03 PM, Fran ois Zielinski francois.zielinski(a)manchester.ac.uk wrote: > Sent to CCL by: "Fran ois Zielinski" [francois.zielinski+/-manchester.ac.uk] > Dear CCLers, > > My current concern is monitoring a dihedral angle evolution from MD runs (DL_POLY HISTORY file, but it can be converted). > PyMOL looks like a possible way of extracting it, or with R scripts perhaps... > However, is there some dedicated tool that enables that sort of analysis? Indeed, a single dihedral stays simple at the moment, but I foresee the need for some more complex operations. > > Best Regards, > Franois> > > From owner-chemistry@ccl.net Tue Oct 15 10:44:00 2013 From: "Emilio Xavier Esposito emilio.esposito ~~ gmail.com" To: CCL Subject: CCL: COMP abstract submission for the Dallas ACS closes Tuesday, October 22, 2013 Message-Id: <-49242-131015104159-7101-4zD1IvDnHVA7hXWtGT4Xhw() server.ccl.net> X-Original-From: Emilio Xavier Esposito Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Oct 2013 10:41:32 -0400 MIME-Version: 1.0 Sent to CCL by: Emilio Xavier Esposito [emilio.esposito|*|gmail.com] Hi The COMP Programming Board would like to remind you that abstract submissions for the COMP technical program at the Dallas ACS meeting **closes at 11pm Central Time on Tuesday, October 22, 2013**. Authors can submit their abstract via . Information about COMP events at the Dallas ACS Meeting (March 16-20, 2014) can be found at the following links: **COMP Symposia at the Dallas ACS meeting** _Member Contributed Symposia_ _Invited Symposia_ **COMP Awards at the Dallas ACS meeting** _NVIDIA GPU Award_ _The Chemical Computing Group Excellence Award for Graduate Students_ _The OpenEye Outstanding Junior Faculty Award in Computational Chemistry_ **Submitting an abstract for the Dallas ACS meeting and Presenter Information** **Organizing a symposium within COMP at a 2015 (or 2016) ACS National Meeting** Thank you for your time The COMP Programming Board Emilio Xavier Esposito Michael Feig Maciej Haranczyk Eric V Patterson Yufeng Jane Tseng Scott A Wildman Follow us on Twitter! http://twitter.com/acsCOMPprog From owner-chemistry@ccl.net Tue Oct 15 11:22:00 2013 From: "Youzhao Lan lyzhao]-[zjnu.cn" To: CCL Subject: CCL: Please recommend me a free software for finding local minimum conforma Message-Id: <-49243-131015111646-32409-BxcFXkHlxfRv3ltCuBHs6g|-|server.ccl.net> X-Original-From: "Youzhao Lan" Date: Tue, 15 Oct 2013 11:16:45 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao\a/zjnu.cn] Dear all, I want to find some local minimum energy conformations of AB produced by interaction between A and B. During interaction, the goemetries of both A and B are assumed to be fixed. For example, A and B are finite-length carbon nanobube and water molecule, respectively. I think I can construct some conformations by hand then optimize them to find some local minimums. Now, I want to find a free software which can automatically do this work. Any help will be appreciated. Youzhao Lan Zhejiang Normal Univ. China From owner-chemistry@ccl.net Tue Oct 15 12:22:00 2013 From: "Francois Zielinski francois.zielinski,+,manchester.ac.uk" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49244-131015120717-4049-fyV5PdQiWFFbe+owHQy1yg(!)server.ccl.net> X-Original-From: Francois Zielinski Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 15 Oct 2013 16:07:08 +0000 MIME-Version: 1.0 Sent to CCL by: Francois Zielinski [francois.zielinski**manchester.ac.uk] Thank you all for your kind replies. For the record, that python script (http://www.ccp5.ac.uk/DL_POLY_CLASSIC/FAQ/his2xyz.py) enables one to convert a HISTORY file into a xyz without the filesize constraint of the package provided utilities. Eventually, I managed to use VMD for bond/angle/dihedral monitoring. I wish this software would be easier to install (had to run it remotely). Unfortunately, I still have 2 problems with it: * atom selection is not that easy through the gui (esp. when laggy), I'll try to find a way to use the vmd cli * No support for DL_POLY_4 HISTORY files... Chimera looks like a nice software, but it has been too much picky on my xyz or pdb files formatting. Did not install Simulaid since file formats are quite restrictive. On PyMOL, it is possible to set up a dihedral measurment, but I could not find any gui way of extracting the values (not even for a single frame). Best Regards François ________________________________________ > From: owner-chemistry+francois.zielinski==manchester.ac.uk() ccl.net [owner-chemistry+francois.zielinski==manchester.ac.uk() ccl.net] on behalf of Paolo Nicolini niko_pd**yahoo.it [owner-chemistry() ccl.net] Sent: Tuesday, October 15, 2013 9:44 AM To: Francois Zielinski Subject: CCL: MD Conformational analysis Sent to CCL by: Paolo Nicolini [niko_pd:-:yahoo.it] Dear Franois, the quick way to monitor a dihedral angle, in my opinion, is with VMD. You simply load your trajectory file, select the 4 atoms from mouse>label, and then you will find the time profile of the dihedral in graphics>labels>dihedrals. You can download VMD here: http://www.ks.uiuc.edu/Research/vmd/ It is for free for academics after registration. Best regards, Paolo ------------------------------------------ Paolo Nicolini, PhD Department of Control Engineering - K335 Faculty of Electrical Engineering Czech Technical University in Prague On 10/14/2013 07:03 PM, Fran ois Zielinski francois.zielinski(a)manchester.ac.uk wrote: > Sent to CCL by: "Fran ois Zielinski" [francois.zielinski+/-manchester.ac.uk] > Dear CCLers, > > My current concern is monitoring a dihedral angle evolution from MD runs (DL_POLY HISTORY file, but it can be converted). > PyMOL looks like a possible way of extracting it, or with R scripts perhaps... > However, is there some dedicated tool that enables that sort of analysis? Indeed, a single dihedral stays simple at the moment, but I foresee the need for some more complex operations. > > Best Regards, > Franoishttp://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 Tue Oct 15 12:56:00 2013 From: "Dr. Vitaly Chaban vvchaban,,gmail.com" To: CCL Subject: CCL: Please recommend me a free software for finding local minimum conforma Message-Id: <-49245-131015122935-4657-m839QZPlYWvEolF0r2bfLQ++server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Oct 2013 18:28:47 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban_._gmail.com] it is pretty unclear what you want this software to do? should it generate initial geometries for further optimization? then it is probably faster to do by hand. Dr. Vitaly V. Chaban On Tue, Oct 15, 2013 at 5:16 PM, Youzhao Lan lyzhao]-[zjnu.cn wrote: > > Sent to CCL by: "Youzhao Lan" [lyzhao\a/zjnu.cn] > Dear all, > I want to find some local minimum energy conformations of AB produced by > interaction between A and B. During interaction, the goemetries of both A and B > are assumed to be fixed. For example, A and B are finite-length carbon nanobube > and water molecule, respectively. I think I can construct some conformations > by hand then optimize them to find some local minimums. Now, I want to find a > free software which can automatically do this work. > > Any help will be appreciated. > > Youzhao Lan > Zhejiang Normal Univ. China> > From owner-chemistry@ccl.net Tue Oct 15 13:38:00 2013 From: "Jim Kress ccl_nospam===kressworks.com" To: CCL Subject: CCL: Accurate vertical ionization energies Message-Id: <-49246-131015133048-14386-sh7Eqn9Y38EoD4VVc4g0bg{:}server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 15 Oct 2013 13:30:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam+*+kressworks.com] Did you try Orca? Not only has it excellent computational capabilities for the phenomena you are calculating, the documentation contains many references that could be of assistance to you. http:///www.cec.mpg.de/downloads Jim -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com%%ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com%%ccl.net] On Behalf Of Scott Mckechnie jsm78|cam.ac.uk Sent: Tuesday, October 15, 2013 6:43 AM To: Kress, Jim Subject: CCL: Accurate vertical ionization energies Sent to CCL by: "Scott Mckechnie" [jsm78 a cam.ac.uk] Dear all, I would like to compare vertical ionization energies obtained from DFT with highly accurate energies computed from a higher level method. I was hoping to get a sense of the accuracy of DFT ionization energies from different functionals and basis sets. I've noticed CCSD(T) is commonly used and I'm wondering what people would recommend. Also, any references would be much appreciated. Best wishes, Scotthttp://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 Tue Oct 15 14:13:01 2013 From: "Ulrike Salzner salzner ~ gmail.com" To: CCL Subject: CCL: Accurate vertical ionization energies Message-Id: <-49247-131015101320-3665-uOoOD51suN1oDCLbTydlDw .. server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary=047d7b676fd09000ce04e8c82e80 Date: Tue, 15 Oct 2013 17:12:59 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner%x%gmail.com] --047d7b676fd09000ce04e8c82e80 Content-Type: text/plain; charset=ISO-8859-1 Dear Scott, I have done work on ionization energies. The work is published in the following papers: Salzner, U.; Baer, R. J. Chem. Phys. 2009, 131, 231101-4. Salzner, U. J. Phys. Chem. A 2010, 114, 10997-11007. Salzner, U.; Aydin, A. J. Chem. Theor. Comput. 2011, 7, 2568-2583. Best regards, Ulrike On Tue, Oct 15, 2013 at 1:43 PM, Scott Mckechnie jsm78|cam.ac.uk < owner-chemistry[-]ccl.net> wrote: > > Sent to CCL by: "Scott Mckechnie" [jsm78 a cam.ac.uk] > Dear all, > > I would like to compare vertical ionization energies obtained from DFT > with highly accurate energies > computed from a higher level method. I was hoping to get a sense of the > accuracy of DFT ionization > energies from different functionals and basis sets. I've noticed CCSD(T) > is commonly used and I'm > wondering what people would recommend. Also, any references would be much > appreciated. > > Best wishes, > > Scott> > > -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --047d7b676fd09000ce04e8c82e80 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Scott,
I have done work on ionization en= ergies. The work is published in the following papers:
Salzner, U.; Baer= , R. J. Chem. Phys. 2009, 131, 231101-4.
Salzner, U. J. Phys. Chem. A 20= 10, 114, 10997-11007.
Salzner, U.; Aydin, A. J. Chem. Theor. Comput. 2011, 7, 2568-2583.
Best regards,
Ulrike


=
On Tue, Oct 15, 2013 at 1:43 PM, Scott Mckechnie= jsm78|cam.ac.uk <owner-chemistry[-]c= cl.net> wrote:

Sent to CCL by: "Scott =A0Mckechnie" [jsm78 a cam.ac.uk]
Dear all,

I would like to compare vertical ionization energies obtained from DFT with= highly accurate energies
computed from a higher level method. I was hoping to get a sense of the acc= uracy of DFT ionization
energies from different functionals and basis sets. I've noticed CCSD(T= ) is commonly used and I'm
wondering what people would recommend. Also, any references would be much a= ppreciated.

Best wishes,

Scott



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--
Assoc. Prof. Ulrike Sal= zner
Department of Chemistry
Bilkent University
06800 Bilkent, Ank= ara
--047d7b676fd09000ce04e8c82e80-- From owner-chemistry@ccl.net Tue Oct 15 15:04:00 2013 From: "Daniel Roe daniel.r.roe ~~ gmail.com" To: CCL Subject: CCL: MD Conformational analysis Message-Id: <-49248-131015131738-3443-TDIrcxdw4aBP+QeWndZEvw[-]server.ccl.net> X-Original-From: Daniel Roe Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 15 Oct 2013 11:17:26 -0600 MIME-Version: 1.0 Sent to CCL by: Daniel Roe [daniel.r.roe---gmail.com] Hi, On Mon, Oct 14, 2013 at 11:03 AM, Fran ois Zielinski francois.zielinski(a)manchester.ac.uk wrote: > My current concern is monitoring a dihedral angle evolution from MD runs (DL_POLY HISTORY file, but it can be converted). You could use ptraj or cpptraj from AmberTools (http://ambermd.org/AmberTools-get.html) to calculate dihedral angles, but you would first have to convert the DL_POLY HISTORY trajectory to a different trajectory format (Amber coordinates/netcdf, Charmm DCD, Scripps binpos, Gromacs TRX, or PDB file with multiple MODELs). For topology, a PDB file would work fine in this case. If I can provide any more assistance let me know. -Dan -- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 201 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-6208 (Fax) From owner-chemistry@ccl.net Tue Oct 15 20:02:00 2013 From: "Youzhao Lan lyzhao() zjnu.cn" To: CCL Subject: CCL: Please recommend me a free software for finding local minimum conf Message-Id: <-49249-131015200119-21405-d4yAQ6mM4ErCG2aUwzOX9g-$-server.ccl.net> X-Original-From: "Youzhao Lan" Date: Tue, 15 Oct 2013 20:01:07 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao##zjnu.cn] Dear Dr. Chaban, Thanks for your help. Yes, I want to have some initial geometries. But I hope these geometries have been automatically pre-optimized by fast methods such as molecular mechanism. Best Lan. ----------------------------------------------------------------------------- --- 2013-10-16 07:54:13 > From: Dr. Vitaly Chaban vvchaban,,gmail.com Date: 2013-10-16 00:28 To: Lan, Youzhao Subject: CCL: Please recommend me a free software for finding local minimum conforma Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban_._gmail.com] it is pretty unclear what you want this software to do? should it generate initial geometries for further optimization? then it is probably faster to do by hand. Dr. Vitaly V. Chaban