From owner-chemistry@ccl.net Sun Aug 24 09:58:00 2014 From: "Dillen, Jan jlmd : sun.ac.za JLMD : sun.ac.za" <owner-chemistry .. server.ccl.net> To: CCL Subject: CCL: Frequencies of Optimized Minima Message-Id: <-50430-140824080554-24406-V61husxkRmr2WU+S+BTKFg .. server.ccl.net> X-Original-From: "Dillen, Jan <jlmd[-]sun.ac.za>" <JLMD[-]sun.ac.za> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 24 Aug 2014 12:05:30 +0000 MIME-Version: 1.0 Sent to CCL by: "Dillen, Jan [jlmd_+_sun.ac.za]" <JLMD_+_sun.ac.za> Matthew, You should tighten the convergence criteria of the minimizer that you are using. For most software, standard convergence criteria are inadequate for calculating accurate vibrational frequencies, especially if the energy surface is flat. If you use DFT, you should make the integration grid finer, whatever program you are using. Use an animation program to show the normal modes that have an imaginary frequency. This may give you a hint on how to go to a minimum. Jan Dillen -----Original Message----- > From: owner-chemistry+jlmd==sun.ac.za:ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za:ccl.net] On Behalf Of Matthew Chen mchen148..aol.com Sent: 22 August 2014 23:57 To: Dillen, Jan <jlmd:sun.ac.za> Subject: CCL: Frequencies of Optimized Minima Sent to CCL by: "Matthew Chen" [mchen148!=!aol.com] Dear Colleagues, I am attempting to perform an optimization on the structures of various enones. The s-trans conformations converged to a minimum without problems; however, the s-cis conformations frequently demonstrate an imaginary frequency. I manually checked the geometry of one of the simpler enones and it looks exactly like the minimum should, so I don't know why this is happening. What factors govern whether a functional will or will not provide imaginary frequencies for minima? What may be done to stop it from doing so? Sincerely, Matthew Chenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThe integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer From owner-chemistry@ccl.net Sun Aug 24 10:33:00 2014 From: "Mozhi M mozhdehm722*|*gmail.com" <owner-chemistry*_*server.ccl.net> To: CCL Subject: CCL: ORCA- stability of scf wavefunctions Message-Id: <-50431-140824032710-15130-G1ai5R/IHj6SvcPEEkQa+A*_*server.ccl.net> X-Original-From: "Mozhi M" <mozhdehm722.:.gmail.com> Date: Sun, 24 Aug 2014 03:27:08 -0400 Sent to CCL by: "Mozhi M" [mozhdehm722]![gmail.com] Dear all I am wonder how could be assure of stability of scf wave functions in ORCA calculations especially in systems checking with more than one multiplicity? thank in advance From owner-chemistry@ccl.net Sun Aug 24 21:46:00 2014 From: "Andrew DeYoung andrewdaviddeyoung[*]gmail.com" <owner-chemistry#%#server.ccl.net> To: CCL Subject: CCL: Obtaining a compilation of OPLS-AA force field parameters Message-Id: <-50432-140824210942-23067-l/GvznfEo2jKzjpeqd4OjQ#%#server.ccl.net> X-Original-From: Andrew DeYoung <andrewdaviddeyoung,,gmail.com> Content-Type: multipart/alternative; boundary=047d7b3a9044073197050169d7e4 Date: Sun, 24 Aug 2014 21:09:34 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung---gmail.com] --047d7b3a9044073197050169d7e4 Content-Type: text/plain; charset=UTF-8 Hi, Does anyone know where I can obtain a compilation of OPLS-AA force field parameters? The OPLS-AA force field has been developed over many years by the Jorgensen Group at Yale. The parameters have been developed and disseminated in many publications over the years. I am wondering if there is a compiled list of all the OPLS-AA parameters. I thought that perhaps the Jorgensen Group website ( http://zarbi.chem.yale.edu/index.html ) might have such a compilation, but I can't seem to find one there. I'm a user of the GROMACS MD package ( http://www.gromacs.org/ ). GROMACS contains library force field files ( usually located in /usr/local/gromacs/share/gromacs/top ), including ones for OPLS-AA. But I'm not sure if these are "official" compilations. There are a lot of comments sprinkled throughout these files, including several that seem to indicate a variety of revisions. Another possible list of parameters is found at the TINKER website: http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm The heading of that file includes this comment: "The parameters supplied with TINKER are from "OPLS All-Atom Parameters for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as provided by W. L. Jorgensen, Yale University during June 2009. These parameters are taken from those distributed with BOSS Version 4.8." So, that list appears to be fairly recent (July 2008 and June 2009). I don't know if there have been many changes/additions to OPLS-AA in the last few years; browsing through the literature, it seems perhaps not. But, nevertheless, does anyone know where I can obtain a fairly recent and official compilation of the OPLS-AA force field parameters? Thank you so very much for your time! Andrew DeYoung Carnegie Mellon University --047d7b3a9044073197050169d7e4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">Hi, <br><br>Does anyone know where I can obtain a compilat= ion of OPLS-AA force field parameters?<br><br>The OPLS-AA force field has b= een developed over many years by the Jorgensen Group at Yale. =C2=A0The par= ameters have been developed and disseminated in many publications over the = years. =C2=A0I am wondering if there is a compiled list of all the OPLS-AA = parameters. =C2=A0I thought that perhaps the Jorgensen Group website ( <a h= ref=3D"http://zarbi.chem.yale.edu/index.html">http://zarbi.chem.yale.edu/in= dex.html</a> ) might have such a compilation, but I can't seem to find = one there.<br> <br>I'm a user of the GROMACS MD package ( <a href=3D"http://www.gromac= s.org/">http://www.gromacs.org/</a> ). =C2=A0GROMACS contains library force= field files ( usually located in /usr/local/gromacs/share/gromacs/top ), i= ncluding ones for OPLS-AA. =C2=A0But I'm not sure if these are "of= ficial" compilations. =C2=A0There are a lot of comments sprinkled thro= ughout these files, including several that seem to indicate a variety of re= visions.<br> <br>Another possible list of parameters is found at the TINKER website:<br>= <br><a href=3D"http://dasher.wustl.edu/tinker/distribution/params/oplsaa.pr= m">http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm</a><br><br= > The heading of that file includes this comment:<br><br>"The parameters= supplied with TINKER are from "OPLS All-Atom Parameters for Organic M= olecules, Ions, Peptides & Nucleic Acids, July 2008" as provided b= y W. L. Jorgensen, Yale University during June 2009. These parameters are t= aken from those distributed with BOSS Version 4.8."<br> <br>So, that list appears to be fairly recent (July 2008 and June 2009). = =C2=A0I don't know if there have been many changes/additions to OPLS-AA= in the last few years; browsing through the literature, it seems perhaps n= ot. =C2=A0But, nevertheless, does anyone know where I can obtain a fairly r= ecent and official compilation of the OPLS-AA force field parameters? =C2= =A0<br> <br>Thank you so very much for your time!<br><br>Andrew DeYoung<br>Carnegie= Mellon University</div> --047d7b3a9044073197050169d7e4--