From owner-chemistry@ccl.net Thu Oct 10 05:30:01 2013 From: "zvitnik zvitnik-x-chem.bg.ac.rs" To: CCL Subject: CCL:G: Gaussian G09- Relaxed scans in Cartesian coordinates Message-Id: <-49230-131010040650-1561-UpOvAv3pUx4OZIgXcZ0gZg*o*server.ccl.net> X-Original-From: zvitnik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 10 Oct 2013 10:06:38 +0200 MIME-Version: 1.0 Sent to CCL by: zvitnik [zvitnik===chem.bg.ac.rs] Hi Jason, Did you check that you do not have co-linear atoms in your z-matrix? Check the angles in you z-matrix to do not have some of them with values near to 0 or 180 degree. Zeljko On 2013-10-10 00:17, Jason Boettger jdb488=psu.edu wrote: > Sent to CCL by: "Jason Boettger" [jdb488!^!psu.edu] > Hi folks! > > This is a humble request for some assistance on a relaxed PES scan in > Gaussian G09 (rev. c01 for what it's worth). I am trying to perform a > relaxed > PES scan to determine the activation energy of an aqueous reaction, > which I > am simulating with several water molecules. When I set up a typical > relaxed > PES scan using ModRedundant commands, my model runs typically crash > after a > few optimization steps (not even scan steps, just the constrained > optimization steps). I believe the shifting of water molecules in my > model > causes the automatically-generated redundant internal coordinate > system to > break, and I get errors of the form "Eigenvalue # is ### should be > less than > 0.000 Eigenvector...Error in redundant internal coordinate system." I > believe > these errors would be fixed if I could manage to do the scan in > Cartesian > coordinates, but ModRedundant commands don't work in Cartesian > coordinates. > This is all very frustrating because it forces me to continually > re-submit > these jobs, wasting precious time in computing queues. > > Well, that is the nature of my problem. Here are some potential > solutions I > have come up with, but I need your help in how to implement them, and > in > knowing if they are even possible: > > First, I could use a sequence of optimization jobs that I string > together > with Link1. I could enter the Cartesian coordinates of all atoms, > then freeze > the two atoms of interest I want to scan (1), then perform a > constrained > optimization in Cartesian coordinates. Then, I could use Link1, > recover the > newly optimized geometry with geom=check guess=read, and then somehow > (2) > modify the Cartesian coordinates of the two atoms of interest so that > they > are closer by, say, 0.1A. Alternatively, I could convert back to > redundant > internal coordinates after each constrained optimization step and do > a one- > step rigid PES scan to increment the two atoms of interest together, > then use > Link1 to switch back to a constrained optimization in Cartesian > coordinates > (3). These proposed solutions would result in very long input files, > but > creating them by means of a Python script should be fairly > straightforward. > My questions are thus: (1) How do you freeze atoms in Cartesian > coordinates? > It is easy to do in redundant internal coordinates, but I couldn't > get any of > the old solutions posted to the CCL list for G03 and earlier to work > for me. > A quick example would be VERY helpful. (2) Is there a way to modify > Cartesian > coordinates that I have recovered with geom=check guess=read? Again, > an > example would be very helpful. (3) Are there any problems in > switching back > and forth between coordinate systems that might arise using this > method? I'd > still need to figure out how to freeze the two atoms of interest. > > Second, I could attempt to work in redundant internal coordinates, > but > manually choose those coordinates which I want to use to describe my > system. > (1) How can I go about constructing these; can anybody point me to a > tutorial? (2) Also, is there a way looking at the error output which > lists > the eigenvectors to tell which redundant internal coordinates are > causing my > issues? > > Third, there could be some magic way to actually do relaxed PES scans > in > Cartesian coordinates. Does anybody know a way? The online GAUSSIAN > manual is > heinously unhelpful at times. > > Thank you so much for making it to the bottom of my long message, and > again, > any help would be appreciated- figuring out how to freeze Cartesian > coordinates would be a big step in the right direction! And let me > know if it > would help for me to clarify anything. Thanks in advance! > > Jason Boettger > PhD Student, Geosciences, Penn State University > jdb488,psu.edu > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Thu Oct 10 08:11:00 2013 From: "Pierre Archirel pierre.archirel[]u-psud.fr" To: CCL Subject: CCL: G09: relaxed scan in cartesian coordinates Message-Id: <-49231-131010072535-32723-6lQRlmlMz9e7UmBL6YZJWg__server.ccl.net> X-Original-From: "Pierre Archirel" Date: Thu, 10 Oct 2013 07:25:34 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel(0)u-psud.fr] This is an answer to J. Boettger Dear colleague, The use of modredundant is (to me) very easy in cartesian coordinates! # ... opt=moderedundant title charge multiplicity atom1 x y z atom2 x y z atom3 x y z .... blank line n1 n3 2. F n1 n2 n3 120. F (n1: number of atom1 in the list...) these data enable the constraint optimisation with the value 2. A of the atom1 atom2 distance and the value 120. degrees for the a1 a2 a3 angle. Is this your question? This is given at page 194 of the g09 manual. Best wishes, Pierre Archirel LCP, Universite Paris-Sud, Orsay, France From owner-chemistry@ccl.net Thu Oct 10 15:38:00 2013 From: "Cory Pye cpye-$-ap.smu.ca" To: CCL Subject: CCL:G: Gaussian G09- Relaxed scans in Cartesian coordinates Message-Id: <-49232-131010153631-16861-xoIa79GrmXtVwMkluDT8iQ^^server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 10 Oct 2013 16:51:22 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye##ap.smu.ca] Jason, It should be possible to use opt=z-matrix to do your relaxed PES scan for the coordinates that you want to vary. For the atoms that move around a lot, you can use cartesians as part of the z-matrix, if needed, to avoid problems with angles becoming 0 or 180. An example might be to use a z-matrix to represent your solute and cartesians to represent the solvating water molecules. -Cory On Wed, 9 Oct 2013, Jason Boettger jdb488=psu.edu wrote: > > Sent to CCL by: "Jason Boettger" [jdb488!^!psu.edu] > Hi folks! > > This is a humble request for some assistance on a relaxed PES scan in > Gaussian G09 (rev. c01 for what it's worth). I am trying to perform a relaxed > PES scan to determine the activation energy of an aqueous reaction, which I > am simulating with several water molecules. When I set up a typical relaxed > PES scan using ModRedundant commands, my model runs typically crash after a > few optimization steps (not even scan steps, just the constrained > optimization steps). I believe the shifting of water molecules in my model > causes the automatically-generated redundant internal coordinate system to > break, and I get errors of the form "Eigenvalue # is ### should be less than > 0.000 Eigenvector...Error in redundant internal coordinate system." I believe > these errors would be fixed if I could manage to do the scan in Cartesian > coordinates, but ModRedundant commands don't work in Cartesian coordinates. > This is all very frustrating because it forces me to continually re-submit > these jobs, wasting precious time in computing queues. > > Well, that is the nature of my problem. Here are some potential solutions I > have come up with, but I need your help in how to implement them, and in > knowing if they are even possible: > > First, I could use a sequence of optimization jobs that I string together > with Link1. I could enter the Cartesian coordinates of all atoms, then freeze > the two atoms of interest I want to scan (1), then perform a constrained > optimization in Cartesian coordinates. Then, I could use Link1, recover the > newly optimized geometry with geom=check guess=read, and then somehow (2) > modify the Cartesian coordinates of the two atoms of interest so that they > are closer by, say, 0.1A. Alternatively, I could convert back to redundant > internal coordinates after each constrained optimization step and do a one- > step rigid PES scan to increment the two atoms of interest together, then use > Link1 to switch back to a constrained optimization in Cartesian coordinates > (3). These proposed solutions would result in very long input files, but > creating them by means of a Python script should be fairly straightforward. > My questions are thus: (1) How do you freeze atoms in Cartesian coordinates? > It is easy to do in redundant internal coordinates, but I couldn't get any of > the old solutions posted to the CCL list for G03 and earlier to work for me. > A quick example would be VERY helpful. (2) Is there a way to modify Cartesian > coordinates that I have recovered with geom=check guess=read? Again, an > example would be very helpful. (3) Are there any problems in switching back > and forth between coordinate systems that might arise using this method? I'd > still need to figure out how to freeze the two atoms of interest. > > Second, I could attempt to work in redundant internal coordinates, but > manually choose those coordinates which I want to use to describe my system. > (1) How can I go about constructing these; can anybody point me to a > tutorial? (2) Also, is there a way looking at the error output which lists > the eigenvectors to tell which redundant internal coordinates are causing my > issues? > > Third, there could be some magic way to actually do relaxed PES scans in > Cartesian coordinates. Does anybody know a way? The online GAUSSIAN manual is > heinously unhelpful at times. > > Thank you so much for making it to the bottom of my long message, and again, > any help would be appreciated- figuring out how to freeze Cartesian > coordinates would be a big step in the right direction! And let me know if it > would help for me to clarify anything. Thanks in advance! > > Jason Boettger > PhD Student, Geosciences, Penn State University > jdb488,psu.edu> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye|*|crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Thu Oct 10 21:32:00 2013 From: "Aaron Deskins nadeskins- -wpi.edu" To: CCL Subject: CCL: Treating sub/super critical water as solvent Message-Id: <-49233-131010213109-15515-WFClny3615vpaWI5NX71kg.@.server.ccl.net> X-Original-From: "Aaron Deskins" Date: Thu, 10 Oct 2013 21:31:06 -0400 Sent to CCL by: "Aaron Deskins" [nadeskins\a/wpi.edu] I am interested in modeling some organic reactions at the DFT level in sub- or super-critical water (near the critical point, high T/high P, or hot compressed water). Ideally I'd like something easy, already implemented in common software. Either I'm not having much luck or this topic hasn't been explored much (I'm guessing the former). I have found a few papers that used the PCM solvation model, adjusting the dielectric constant to the appropriate value of water under these conditions. This would be a great method since it is easy to use. I'd like to avoid an explicit water solvent model if possible. Any suggestions? Thank you, Aaron