From owner-chemistry@ccl.net Wed Oct 9 11:05:01 2013 From: "Jerome Kieffer Jerome.Kieffer%%terre-adelie.org" To: CCL Subject: CCL: Nobel price in Chemistry !!! Message-Id: <-49227-131009093027-27597-BZ2PDxfzDubKuc1+M4m0qQ|-|server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Wed, 9 Oct 2013 15:30:03 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [Jerome.Kieffer^^^terre-adelie.org] Congratulation to Martin Karplus, Michael Levitt & Arieh Warshel ! -- Jerome Kieffer From owner-chemistry@ccl.net Wed Oct 9 12:59:00 2013 From: "jaleel uc jaleel.uc()gmail.com" To: CCL Subject: CCL: Nobel price in Chemistry !!! Message-Id: <-49228-131009123549-4787-uZraF/Q89COm9qfKgTejMQ[#]server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=089e0115eb5aeea3d904e851791f Date: Wed, 9 Oct 2013 22:05:42 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc(_)gmail.com] --089e0115eb5aeea3d904e851791f Content-Type: text/plain; charset=ISO-8859-1 http://www.youtube.com/watch?v=csxKNLm2bhM On Wed, Oct 9, 2013 at 7:00 PM, Jerome Kieffer Jerome.Kieffer%% terre-adelie.org wrote: > > Sent to CCL by: Jerome Kieffer [Jerome.Kieffer^^^terre-adelie.org] > Congratulation to Martin Karplus, Michael Levitt & Arieh Warshel ! > > -- > Jerome Kieffer > > -- JALEEL --089e0115eb5aeea3d904e851791f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable


On Wed, Oct 9, 2013 at 7:00 PM,= Jerome Kieffer Jerome.Kieffer%%terre-a= delie.org <owner-chemistry|,|ccl.net> wrote:

Sent to CCL by: Jerome Kieffer [Jerome.Kieffer^^^terre-adelie.org]
Congratulation to Martin Karplus, Michael Levitt & Arieh Warshel !

--
Jerome Kieffer <Jerome.Kieffer-*-terre-adelie.org>



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=A0JALEEL
--089e0115eb5aeea3d904e851791f-- From owner-chemistry@ccl.net Wed Oct 9 20:27:00 2013 From: "Jason Boettger jdb488=psu.edu" To: CCL Subject: CCL:G: Gaussian G09- Relaxed scans in Cartesian coordinates Message-Id: <-49229-131009181753-15814-Sge8/9VnJh/tw35LDCb/OQ\a/server.ccl.net> X-Original-From: "Jason Boettger" Date: Wed, 9 Oct 2013 18:17:52 -0400 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