From owner-chemistry@ccl.net Thu Jan 26 06:58:00 2012 From: "Saman Mandegar mandegar_saman[]yahoo.com" To: CCL Subject: CCL: G)9: QST2 command and interpolation Message-Id: <-46195-120126065613-12935-/lelrDBian4OsxED/sa47A=server.ccl.net> X-Original-From: "Saman Mandegar" Date: Thu, 26 Jan 2012 06:56:11 -0500 Sent to CCL by: "Saman Mandegar" [mandegar_saman]![yahoo.com] Dear All, I have a molecule with two structures. The difference between first and second structure is just twisting along a torsion angle. I want to find some structures between these two by interpolation of internal coordinates. I dont want to optimize the structures. I expected to find some options in QST2 command to get the intermediate structures? Any help is greatly appreciated. Thank you in advance. Best regards, Saman From owner-chemistry@ccl.net Thu Jan 26 10:12:00 2012 From: "Jason D Acchioli jdacchio_+_gmail.com" To: CCL Subject: CCL:G: Unusual imaginary frequencies in ORCA Message-Id: <-46196-120126101046-26722-qyZaunM+//1Cjl062C2xTA:+:server.ccl.net> X-Original-From: "Jason D'Acchioli" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 26 Jan 2012 09:10:34 -0600 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: "Jason D'Acchioli" [jdacchio*o*gmail.com] Hi CCL-ers, I'm having fits over the results of vibrational analyses of some organometallic species in ORCA 2.8. I've been running calcs on eta5-coordinated cyclopentadienyl and indenyl species, and keep coming up with 12 imaginary vibrational modes. I've used Grid6 and Grid7, both with VeryTightSCF, but I keep getting the same results. It is interesting to note that in the ORCA output, I get the message: The first frequency considered to be a vibration is 20 The total number of vibrations considered is 31 Frequency number 20 is the first real frequency in the file. So do I ignore the imaginary vibrational frequencies? As an aside, I don't get the same vibrational results using Gaussian09 or Gamess (Guassian calculates frequencies analytically, and Gamess using semi-numerical methods). Please help! I'd like to be able to use ORCA for these calcs, but I'm not sure why I keep getting imaginary modes! Jason PS The input file is: #Geometry optimization of eta-5 cp Fe complex; ! PAL8 RKS B3LYP/G ECP{SDD=Fe, SD(10,MDF)} def2-SVP VeryTightSCF Grid6 moread NoFinalGrid %moinp "eta5_cp_fe_cat.inp_374.rat1.uwsp.gbw" !NumFreq %freq CentralDiff true end *xyz 1 1 C 0.971689 0.719105 1.589637 C 0.977762 -0.702168 1.606407 C -0.400171 1.150321 1.594023 C -1.221910 -0.005615 1.599239 C -0.374426 -1.161652 1.578488 H -0.749285 2.182860 1.606905 H -2.312277 -0.012064 1.604646 H -0.701906 -2.200605 1.595688 C -1.475017 -0.471787 -1.147495 C 0.341691 1.519012 -1.134741 C 1.139269 -1.047892 -1.139251 O -2.398822 -0.777188 -1.727932 O 0.566217 2.472894 -1.703417 O 1.854371 -1.711141 -1.715752 H 1.866252 -1.334418 1.615166 H 1.849699 1.364293 1.609103 Fe -0.002414 0.002238 -0.169933 * ******************************************* Jason D'Acchioli Assistant Professor of Chemistry University of Wisconsin-Stevens Point 2001 Fourth Avenue Stevens Point, WI 54481 http://chemdac.uwsp.edu From owner-chemistry@ccl.net Thu Jan 26 11:54:01 2012 From: "De Luca Giorgio g.deluca---itm.cnr.it" To: CCL Subject: CCL: solvation energies Message-Id: <-46197-120126055513-15121-yG5DdpoVdA8JFolNT99mUw _ server.ccl.net> X-Original-From: "De Luca Giorgio" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 26 Jan 2012 11:54:29 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "De Luca Giorgio" [g.deluca{}itm.cnr.it] Dear all, I would like to ask if anyone knows the solvation energies (DG or/and DH) of p-coumaric acid and pinobanksin in water or/and ethanol. If someone can send me some references to find these values ​I would be very grateful. Thank you for your attention. Best regards Giorgio From owner-chemistry@ccl.net Thu Jan 26 13:15:00 2012 From: "Rudolf Herrmann rudolf.herrmann*|*physik.uni-augsburg.de" To: CCL Subject: CCL:G: Unusual imaginary frequencies in ORCA Message-Id: <-46198-120126122149-21207-USeG1b40azQofaGIUdny1Q#%#server.ccl.net> X-Original-From: "Rudolf Herrmann" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 26 Jan 2012 18:21:41 +0100 MIME-Version: 1.0 Sent to CCL by: "Rudolf Herrmann" [rudolf.herrmann/./physik.uni-augsburg.de] Hello Jason, > > I'm having fits over the results of vibrational analyses of some > organometallic species in ORCA 2.8. I've been running calcs on > eta5-coordinated cyclopentadienyl and indenyl species, and keep coming up > with 12 imaginary vibrational modes. I've used Grid6 and Grid7, both with VeryTightSCF, but I keep getting the same results. It is interesting > to note that in the ORCA output, I get the message: > > The first frequency considered to be a vibration is 20 > The total number of vibrations considered is 31 > > Frequency number 20 is the first real frequency in the file. So do I > ignore the imaginary vibrational frequencies? > > As an aside, I don't get the same vibrational results using Gaussian09 or > Gamess (Guassian calculates frequencies analytically, and Gamess using semi-numerical methods). Please help! I'd like to be able to use ORCA for > these calcs, but I'm not sure why I keep getting imaginary modes! > > Jason > I recently had a similar problem (due to diffuse basis functions) which I reported to the ORCA list. Christoph Riplinger from the ORCA team noted that I did not have good SCF convergence (Energy was converted but not DP-MAX) which created the awkward frequency results. This could also be your case. Maybe you can get better convergence by enforcing convergence of all criteria with %scf convcheckmode 0 maxiter 1000 end Hope this helps, R. Herrmann. -- Dr. Rudolf Herrmann Institut für Physik Universität Augsburg > PS The input file is: > > #Geometry optimization of eta-5 cp Fe complex; > ! PAL8 RKS B3LYP/G ECP{SDD=Fe, SD(10,MDF)} def2-SVP VeryTightSCF Grid6 moread NoFinalGrid > > %moinp "eta5_cp_fe_cat.inp_374.rat1.uwsp.gbw" > > !NumFreq > > %freq CentralDiff true end > > *xyz 1 1 > C 0.971689 0.719105 1.589637 > C 0.977762 -0.702168 1.606407 > C -0.400171 1.150321 1.594023 > C -1.221910 -0.005615 1.599239 > C -0.374426 -1.161652 1.578488 > H -0.749285 2.182860 1.606905 > H -2.312277 -0.012064 1.604646 > H -0.701906 -2.200605 1.595688 > C -1.475017 -0.471787 -1.147495 > C 0.341691 1.519012 -1.134741 > C 1.139269 -1.047892 -1.139251 > O -2.398822 -0.777188 -1.727932 > O 0.566217 2.472894 -1.703417 > O 1.854371 -1.711141 -1.715752 > H 1.866252 -1.334418 1.615166 > H 1.849699 1.364293 1.609103 > Fe -0.002414 0.002238 -0.169933 > * > > > ******************************************* > Jason D'Acchioli > Assistant Professor of Chemistry > University of Wisconsin-Stevens Point > 2001 Fourth Avenue > Stevens Point, WI 54481 > http://chemdac.uwsp.edu> > > From owner-chemistry@ccl.net Thu Jan 26 14:24:00 2012 From: "Vera Cathrine vera.cathrine###yahoo.com" To: CCL Subject: CCL:G: CASSCF error in G03 Message-Id: <-46199-120126123411-11646-B0lBIVMRKZJkBFfJ6d+T+Q]*[server.ccl.net> X-Original-From: "Vera Cathrine" Date: Thu, 26 Jan 2012 12:34:09 -0500 Sent to CCL by: "Vera Cathrine" [vera.cathrine*|*yahoo.com] Dear CCL Users, I am running a casscf calculation in G03 and my route section is as following. I just read orbitals from a previous CAS(14,13) calculation and altered two orbitals. The reason is that I want to reduce the cas space from 1413 (full active space ) to reduced one 1212. #p casscf(12,12)/3-21g nosymm geom=connectivity guess=(read,alter) pop=full But I got this kind of error in l401: (Enter /home/mdavari/g03/l401.exe) Initial guess read from the checkpoint file: input.chk Guess basis will be translated and rotated to current coordinates. Unexpected end-of-file while reading orbital switches. Error termination via Lnk1e in /home/vcathrine/g03/l401.exe at Thu Jan 26 17:48:28 2012. Could anybody tell me why this kind of generic error occurs? Thank you in advance, Regrads, Vera From owner-chemistry@ccl.net Thu Jan 26 14:59:00 2012 From: "Vera Cathrine vera.cathrine__yahoo.com" To: CCL Subject: CCL:G: CASSCF error in G03 Message-Id: <-46200-120126120555-23341-uaZpWCma980pYwcoVlFKpw|-|server.ccl.net> X-Original-From: "Vera Cathrine" Date: Thu, 26 Jan 2012 12:05:54 -0500 Sent to CCL by: "Vera Cathrine" [vera.cathrine(0)yahoo.com] Dear CCL Users, I am running a casscf calculation in G03 and my route section is as following. I just read orbitals from a previous CAS(14,13) calculation and altered two orbitals. The reason is that I want to reduce the cas space from 1413 (full active space ) to reduced one 1212. #p casscf(12,12)/3-21g nosymm geom=connectivity guess=(read,alter) pop=full But I got this kind of error in l401: (Enter /home/mdavari/g03/l401.exe) Initial guess read from the checkpoint file: input.chk Guess basis will be translated and rotated to current coordinates. Unexpected end-of-file while reading orbital switches. Error termination via Lnk1e in /home/vcathrine/g03/l401.exe at Thu Jan 26 17:48:28 2012. Could anybody tell me why this kind of generic error occurs? Thank you in advance, Regrads, Vera From owner-chemistry@ccl.net Thu Jan 26 17:21:00 2012 From: "Billy McCann bwm0005#%#tigermail.auburn.edu" To: CCL Subject: CCL:G: G)9: QST2 command and interpolation Message-Id: <-46201-120126153042-32407-bvUGZXQ54wNX6W7bCBH09w . server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 26 Jan 2012 20:30:04 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005^-^tigermail.auburn.edu] Saman, The `scan` keyword may be what you're looking for. See [1]. This is appropriate if you are not wanting to optimize the structures at each point along the rotation, i.e. a "rigid" scan. For a "relaxed" scan, in which each point along the rotation would be optimized, see `opt=modredundant` [2]. QST2 is designed for locating a transition structure, given the initial and final geometries. [1] http://www.gaussian.com/g_tech/g_ur/k_scan.htm [2] http://www.gaussian.com/g_tech/g_ur/k_opt.htm Hope that helps. +++++++++++++++++++ Billy Wayne McCann Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu*ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu*ccl.net] On Behalf Of Saman Mandegar mandegar_saman[]yahoo.com Sent: Thursday, January 26, 2012 5:56 AM To: Billy McCann Subject: CCL: G)9: QST2 command and interpolation Sent to CCL by: "Saman Mandegar" [mandegar_saman]![yahoo.com] Dear All, I have a molecule with two structures. The difference between first and second structure is just twisting along a torsion angle. I want to find some structures between these two by interpolation of internal coordinates. I dont want to optimize the structures. I expected to find some options in QST2 command to get the intermediate structures? Any help is greatly appreciated. Thank you in advance. Best regards, Samanhttp://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 Thu Jan 26 17:56:00 2012 From: "Dmytro Bykov dbykov||mpi-mail.mpg.de" To: CCL Subject: CCL: Unusual imaginary frequencies in ORCA Message-Id: <-46202-120126161846-12968-thytXFEl2Yy3jjI1HZ1OzQ-,-server.ccl.net> X-Original-From: Dmytro Bykov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 Jan 2012 22:18:39 +0100 MIME-Version: 1.0 Sent to CCL by: Dmytro Bykov [dbykov*mpi-mail.mpg.de] Dear Jason, I ran your job with new ORCA2.9 and had no problem. Only one imaginary frequency -7 cm^-1 was in my output. Such small imaginary frequency is just numerical noise, as ORCA differentiate analytical gradient numerically. I also don't think you can have problems with convergence as Rudolf Hermann suggested, since you are using smaller basis set. In my calculation i had no problem with convergence. To solve your problem more information is needed. The best way is to go to the ORCA forum http://www.thch.uni-bonn.de/tc/orca/index.php?option=com_joobb&view=board&la and post there your problem with additional information (output from your calculation would be nice). Hope to see you in ORCA forum! Dima Bykov From owner-chemistry@ccl.net Thu Jan 26 18:53:00 2012 From: "Joy Ku joyku*_*stanford.edu" To: CCL Subject: CCL: Workshop: MD Prototyping & Simulations on GPUs with OpenMM - New Date Message-Id: <-46203-120126184845-28692-DtAmMLLO0lDDc3/R3Evatg###server.ccl.net> X-Original-From: "Joy Ku" Date: Thu, 26 Jan 2012 18:48:41 -0500 Sent to CCL by: "Joy Ku" [joyku]|[stanford.edu] Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. Where: Stanford University When: Mar. 12-13, 2012 ***NEW DATES*** Registration: Free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshops.htm. OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs). And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. For the workshop, no programming background is required, though programming topics will also be covered for those who are interested in them. During the workshop, you will gain hands-on experience using OpenMMs new application layer and application programming interface (API). Learn to: * Set up and run an MD simulation on your GPU using both PDB and AMBER files * Create a custom force to apply to your simulations * Customize the simulation through Python scripting You will also have time to work with the OpenMM development team on your own research project. ________________________________________ OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. [2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.