From owner-chemistry@ccl.net Tue Feb 24 04:37:01 2009 From: "Egbert Zojer egbert.zojer ~~ tugraz.at" To: CCL Subject: CCL: k point mesh Message-Id: <-38712-090224041124-20222-rJ6uWjhxiWd+5G17dcRIog.@.server.ccl.net> X-Original-From: Egbert Zojer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Feb 2009 09:28:34 +0100 MIME-Version: 1.0 Sent to CCL by: Egbert Zojer [egbert.zojer{}tugraz.at] Dear David, Let me just add a comment regarding a 3-D periodic code used to calculate SAMs on a surface in the slab approach - I guess that this is the second set of calculations you are referring to - the ones with the other k-point mesh (like 8x8x1), which have been performed with VASP or SIESTA with true 3D periodic boundary conditions - which is possible as in such cases never any voltage is applied in z-direction: In this context you need to remember what the wavefunctions with k-vectors different from zero mean. In a Bloch-wave you are always dealing with a lattice periodically modulated plane wave and the k is related to the wavenumber of that plane wave. A wavefunction with k=0 is exactly the same in each unit cell, a k-value at the Brillouin zone edge gives you 180° phase shifted wave functions in each unit cell. You could approximately also immagine it like this: The k-value represents the phase relation between the values a Bloch-type wavefunction has in different unit cells. When you run slab-type calculations on surfaces, you do not "want to know" the relationship between different slabs, as the fact that there are slabs stacked on top of each other is an artifact of the specific model you have to choose to use a 3D-periodic band-structure code. So in such calculations, you typically introduce a large enough vacuum gap between the slabs to avoid any interaction between the slabs. But then it also is not necessary to calculate more than one k-pont in that direction (typically the z-direction). If you introduce a large enough gap between the slabs, there will also be no dispersion in the kz direction. How many k-points you need in x- and y-direction you need to figure out for your particular system (i.e., you need to increase that number until you reach convergence). For typical problems 8 x 8 x 1 appears reasonabl. regards, Egbert Anders Blom anders.blom*o*quantumwise.com schrieb: > Sent to CCL by: Anders Blom [anders.blom^^^quantumwise.com] > Hello David, > > the literature you refer to is most likely calculations performed using > TranSIESTA (Brandbyge et al., Phys. Rev. B 65, 165401 (2002)) or a > similar code that uses the same methodology (e.g. Atomistix ToolKit or > Smeagol, although I am not familiar with the deeper details of the > latter software). > > The key point of this method is that the boundary conditions are > actually not periodic in the z direction. Instead, open boundary > conditions are used, in order to apply a voltage across the structure, > so that one can compute the electron current under finite bias. The > system (a so-called two-probe) is subdivided into three parts, left and > right electrodes, which are bulk-like (semi-infinite), and a central > scattering region over which the bias is actually applied, and where the > non-equilibrium electron distribution can be computed using Green's > function techniques. > > To understand why one needs many Kz-points in this case, assume that you > have an ideal system, i.e. the electrodes are identical > to the central region. Let HL, HC, HR be the Hamiltonian of the left > electrode, central region, and right electrode, respectively. HL, HR are > calculated under periodic boundary conditions, while HC is evaluated > (self-consistently) calculated with open boundary conditions using > self-energies obtained from HL and HR. > > Now, clearly you will only get integer transmission in this system if > HL=HR=HC. To obtain this, the same k-point sampling should be used in > the Kx and Ky directions for the electrode and subsequent two-probe > calculation (with open boundary conditions). This point is quite trivial. > > In the z-direction, however, the two-probe calculation corresponds to an > infinite number of Kz points, thus you need a lot of k-points in the > z-direction for the electrode calculation to ensure the same level of > accuracy. > > Generally, the literature values for Kz may be a little conservative, > but it is relatively inexpensive since these k-points are only required > for the electrode calculation which is the smaller and faster part of > the whole computation. > > In case you have specific questions about or general interest in > Atomistix ToolKit, you can also post questions on its official user > forum, http://quantumwise.com/forum. > > Anders Blom > > -- -------------------------------------------------------------------- A.o. Univ.-Prof. DI Dr. Egbert Zojer Institute of Solid State Physics Graz University of Technology Petersgasse 16, A-8010 Graz, AUSTRIA -------------------------------------------------------------------- e-mail: egbert.zojer|a|tugraz.at Tel.: ++43/316/873-8475 (FAX: -8466) http://www.if.tugraz.at -------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Feb 24 10:01:00 2009 From: "Tapta Kanchan Roy taptakanchan:gmail.com" To: CCL Subject: CCL: van der waal radius by ab-initio method Message-Id: <-38713-090223074608-20465-kt2YMBDyE0MtFOL8fZ67Ng]^[server.ccl.net> X-Original-From: Tapta Kanchan Roy Content-Type: multipart/alternative; boundary=001636b430fb41011f04639562c4 Date: Mon, 23 Feb 2009 18:15:56 +0530 MIME-Version: 1.0 Sent to CCL by: Tapta Kanchan Roy [taptakanchan-*-gmail.com] --001636b430fb41011f04639562c4 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all, I would be grateful if anyone can suggest me a name of a software package which can calculate *van der waal radius by ab-initio* method. Thanks in advance. T. K. Roy -- ************************************************************************************************************** " Try your best to get whatever you love. Otherwise, you will be forced to love whatever you get. " ************************************************************************************************************** Regards, Tapta Kanchan Roy C/O Prof. M. Durga Prasad,s Lab School of Chemistry University of Hyderabad Hyderabad-500046 India --001636b430fb41011f04639562c4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi all,
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Thanks in advance.
T. K. Roy
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= --
********************************************************************= ******************************************
" Try your best to get w= hatever you love. Otherwise, you will be forced to love whatever you get. &= quot;
***************************************************************************= ***********************************
Regards,

Tapta Kanchan RoyC/O Prof. M. Durga Prasad,s Lab
School of Chemistry
University of Hy= derabad
Hyderabad-500046
India


--001636b430fb41011f04639562c4-- From owner-chemistry@ccl.net Tue Feb 24 19:58:00 2009 From: "Joe Leonard jleonard42 * gmail.com" To: CCL Subject: CCL: Looking for ring formation: hit to lead Message-Id: <-38714-090224195616-7601-++WUUbFq+TBCYyXTIq1BFg(_)server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 24 Feb 2009 19:55:49 -0500 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Joe Leonard [jleonard42]-[gmail.com] Folks, I am looking into scaffold hopping/scaffold extension tools, and wonder whether anybody can suggest a reference (modeling or med- chem) where the scaffold of the initial hit(s) were expanded via ring fusion or substitution before the final lead(s) were created. I've been checking the de novo literature, but I worry they're overly concerned with modeling/methodology and not paying enough attention to the chemical problems being solved. I would greatly appreciate any pointers you might have where such project chemistry is discussed... Thanks in advance! Joe Leonard jleonard42=-=gmail.com -- If the lessons of history teach us anything it is that nobody learns the lessons that history teaches us. From owner-chemistry@ccl.net Tue Feb 24 20:33:00 2009 From: "John McKelvey jmmckel(-)gmail.com" To: CCL Subject: CCL: van der waal radius by ab-initio method Message-Id: <-38715-090224141827-5990-sZ0aopmznGkSL1n5yRqRYg*o*server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=000e0cd2e12c1bef370463aefb12 Date: Tue, 24 Feb 2009 14:18:15 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel(-)gmail.com] --000e0cd2e12c1bef370463aefb12 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit *One way to estimate is to compute an atomic volume at ~0.001 outer density contour and solve for R at 1.333*pi*R^3.* John McKelvey On Mon, Feb 23, 2009 at 7:45 AM, Tapta Kanchan Roy taptakanchan:gmail.com < owner-chemistry{=}ccl.net> wrote: > > Hi all, > I would be grateful if anyone can suggest me a name of a software > package which can calculate *van der waal radius by ab-initio* method. > Thanks in advance. > T. K. Roy > > > > > > > -- > > ************************************************************************************************************** > " Try your best to get whatever you love. Otherwise, you will be forced to > love whatever you get. " > > ************************************************************************************************************** > Regards, > > Tapta Kanchan Roy > C/O Prof. M. Durga Prasad,s Lab > School of Chemistry > University of Hyderabad > Hyderabad-500046 > India > > > --000e0cd2e12c1bef370463aefb12 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 
One way to estimate is to compute an atomic volume at ~0.001 outer =
density 
contour and solve for R at 1.333*pi*R^3.
John McKe= lvey

On Mon, Feb 23, 2009 at 7:45 AM, Tap= ta Kanchan Roy taptakanchan:gmail.com <owner-chemistr= y{=}ccl.net> wrote:

Hi all,
=A0=A0=A0=A0=A0=A0=A0=A0 I would be grateful if anyone can sug= gest me a name of a software package which can calculate=A0 van der waal= radius by ab-initio method.
Thanks in advance.
T. K. Roy
=A0=A0=A0=A0=A0=A0=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0




--
********************= ***************************************************************************= ***************
" Try your best to get whatever you love. Otherwise= , you will be forced to love whatever you get. "
***************************************************************************= ***********************************
Regards,

Tapta Kanchan RoyC/O Prof. M. Durga Prasad,s Lab
School of Chemistry
University of Hy= derabad
Hyderabad-500046
India



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