From owner-chemistry@ccl.net Mon Dec 1 13:40:01 2014 From: "Mikael Johansson mikael.johansson(0)iki.fi" To: CCL Subject: CCL: Jmol script for plotting 3D vectors on molecules: jvec2jmol Message-Id: <-50784-141201132704-18194-9zUnCXGfQDLavvFBqBypyA * server.ccl.net> X-Original-From: Mikael Johansson Content-Type: multipart/mixed; BOUNDARY="-696237619-668693063-1417458413=:6328" Date: Mon, 1 Dec 2014 20:26:53 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson[]iki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696237619-668693063-1417458413=:6328 Content-Type: text/plain; format=flowed; charset=ISO-8859-15 Content-Transfer-Encoding: 8BIT Hello All, Just in case someone happens to find it useful: I couldn't find a quick and simple way to visualize vector data together with molecules, especially in 3D; while the failure might very well be due to a deficiency in googling skill, I made an attempt at creating a tool. If you have a file wih vector data in six columns, in the simple format x.coord y.coord z.coord d.x d.y d.z the jvec2jmol script transform the vectors into Jmol script form for quick visualization. At simplest, the syntax would be: jvec2jmol.py data.txt data.jmol; jmol -s data.jmol You will probably want to display some molecule as well, of course. The default values of the script are biased towards displaying magnetically induced current vectors, but are easily adjustable. jvec2jmol has a few colour gradient options, and a rudimentary understanding of translucency. It even comes with a quick but not necessarily dirty mini-tutorial. The script can be downloaded here; the .tar.gz file contains some simple examples: http://www.iki.fi/~mpjohans/scripts/ Of course, comments, bug reports, etc, are welcome. Cheers, Mikael J. -- Dr. Mikael Johansson Computational Biocatalysis Department of Chemistry Technische Universität München mikael.johansson .. iki.fi http://www.iki.fi/~mpjohans/ ---696237619-668693063-1417458413=:6328-- From owner-chemistry@ccl.net Mon Dec 1 14:37:01 2014 From: "Igors Mihailovs igors.mihailovs0++gmail.com" To: CCL Subject: CCL:G: Freezing the density of a fragment Message-Id: <-50785-141201141658-17727-ZcdsQ4KBQdws4tc6NHn4Ng[-]server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=089e0158b86a80dd2f05092bb1d1 Date: Mon, 1 Dec 2014 20:22:08 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0 . gmail.com] --089e0158b86a80dd2f05092bb1d1 Content-Type: text/plain; charset=UTF-8 Good day to everybody, Is it possible to freeze electron density of some fragment during a multi-molecular calculation, treating this fragment only as a source of external potential? In Gaussian or some another program? Because it would let us to run some very costly calculations, iteratively optimizing electron density of each part... Thanks in advance! With best regards, Igors Mihailovs Institute of Solid State Physics, University of Latvia --089e0158b86a80dd2f05092bb1d1 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Good day to everybody,

Is it possible to= freeze electron density of some fragment during a multi-molecular calculat= ion, treating this fragment only as a source of external potential? In Gaus= sian or some another program? Because it would let us to run some very cost= ly calculations, iteratively optimizing electron density of each part... Th= anks in advance!

With best regards,
Igors Mihailovs
Institute of Solid S= tate Physics,
University of Latvia<= br>

--089e0158b86a80dd2f05092bb1d1-- From owner-chemistry@ccl.net Mon Dec 1 18:45:01 2014 From: "Fedor Goumans goumans]-[scm.com" To: CCL Subject: CCL:G: Freezing the density of a fragment Message-Id: <-50786-141201162906-12123-JZnyi3qFLczR9KNSDtkp5A ~~ server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 01 Dec 2014 22:28:58 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans .. scm.com] Dear Igor, You can use Frozen-Density Embedding, or subsystem DFT, with ADF to do just that. In the current implementation you can freeze the densities of different subsystems so long as they are not covalently bound (with the exception of '3-FDE' as applied to proteins). Look at papers by (amongst others) Christoph Jacob, Johannes Neugebauer, Michele Pavanello, Luuk Visscher, Tomasz Wesolowski on the implementation in ADF and various applications. A recent review: Jacob & Neugebauer, WIREs:CMS 4, 325 (2013) (doi: 10.1002/wcms.1175) With kind regards, Fedor On 12/1/2014 7:22 PM, Igors Mihailovs igors.mihailovs0++gmail.com wrote: > Good day to everybody, > > Is it possible to freeze electron density of some fragment during a > multi-molecular calculation, treating this fragment only as a source > of external potential? In Gaussian or some another program? Because it > would let us to run some very costly calculations, iteratively > optimizing electron density of each part... Thanks in advance! > > With best regards, > Igors Mihailovs > Institute of Solid State Physics, > University of Latvia > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 https://www.scm.com https://twitter.com/SCM_Amsterdam