CCL: Water Molecule Simulation

From owner-chemistry@ccl.net Mon Jan 19 06:01:00 2009 From: "Leyla Ramin l.ramin,,aeromech.usyd.edu.au" To: CCL Subject: CCL: Water Molecule Simulation Message-Id: <-38456-090119054444-13769-zAlRR4w4twQCrbh6X+RJVA::server.ccl.net> X-Original-From: "Leyla Ramin" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C97A22.E24B1CFD" Date: Mon, 19 Jan 2009 21:43:34 +1100 MIME-Version: 1.0 Sent to CCL by: "Leyla Ramin" [l.ramin*aeromech.usyd.edu.au] This is a multi-part message in MIME format. ------_=_NextPart_001_01C97A22.E24B1CFD Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, Thanks for your reply, However I have problem with Tinker installation, = Would you please send me the code of water simulation. =20 Kind Regards Leyla Ramin ________________________________ > From: owner-chemistry+lram5228=3D=3Dusyd.edu.au*o*ccl.net on behalf of = Lukasz Cwiklik cwiklik .. gmail.com Sent: Sun 18/01/2009 22:33 To: Leyla Ramin Subject: CCL: Water Molecule Simulation Sent to CCL by: Lukasz Cwiklik [cwiklik:_:gmail.com] On Sat, Jan 17, 2009 at 1:57 AM, Kianoush Mirsanaei k.mirsanaie!=3D!yahoo.com wrote: > > Sent to CCL by: "Kianoush Mirsanaei" [k.mirsanaie()yahoo.com] > Hello Everybody, > > I am asking if anybody can advise me with the fortran code of water = molecules simulation(To calculate forces and potential). Dear Kianoush, If you want to make MD or MC simulations of water try Gromacs or TINKER (both free and written in Fortran). If you want to calculate intermolecular potentials - just find it in the literature, at the beginning, take a look at: http://www.lsbu.ac.uk/water/molecule.html and: http://www.lsbu.ac.uk/water/models.html and references therein. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com =20 -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt------_=_NextPart_001_01C97A22.E24B1CFD Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL: Water Molecule Simulation=0A= =0A= =0A= =0A=

=0A=

Hello,

=0A=

Thanks for your reply, = However I have problem with Tinker installation, Would you please send = me the code of water simulation.

=0A=

=0A=

Kind Regards=0A=
Leyla Ramin

=0A=

=0A=

=0A= From: = owner-chemistry+lram5228=3D=3Dusyd.edu.au*o*ccl.net on behalf of Lukasz = Cwiklik cwiklik .. gmail.com
Sent: Sun 18/01/2009 = 22:33
To: Leyla Ramin
Subject: CCL: Water Molecule = Simulation

=0A=

=0A=

Sent to CCL by: Lukasz Cwiklik = [cwiklik:_:gmail.com]
On Sat, Jan 17, 2009 at 1:57 AM, Kianoush = Mirsanaei
k.mirsanaie!=3D!yahoo.com <owner-chemistry[*]ccl.net> = wrote:
>
> Sent to CCL by: "Kianoush Mirsanaei" = [k.mirsanaie()yahoo.com]
> Hello Everybody,
>
> I am = asking if anybody can advise me with the fortran code of water molecules = simulation(To calculate forces and potential).

Dear = Kianoush,
If you want to make MD or MC simulations of water try = Gromacs or
TINKER (both free and written in Fortran).
If you want = to calculate intermolecular potentials - just find it in
the = literature,
at the beginning, take a look at:
http://www.lsbu.ac.uk/= water/molecule.html
and:
http://www.lsbu.ac.uk/wa= ter/models.html
and references = therein.

Best,
Lukasz

--
Lukasz Cwiklik
http://cwiklik.wordpress.com

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<= /BODY> ------_=_NextPart_001_01C97A22.E24B1CFD-- From owner-chemistry@ccl.net Mon Jan 19 06:35:01 2009 From: "Wendy A Warr wendy:+:warr.com" To: CCL Subject: CCL: Articles in InChI and on cheminformatics education Message-Id: <-38457-090119063110-31460-sGUO2sZgdih+gQ+9RbyHhg[A]server.ccl.net> X-Original-From: "Wendy A Warr" Date: Mon, 19 Jan 2009 06:31:05 -0500 Sent to CCL by: "Wendy A Warr" [wendy{=}warr.com] My latest column on QSARWorld.com describes the state-of-the-art of the IUPAC Chemical Identifier, InChI. http://www.qsarworld.com/INCHI1.php The previous column covered cheminformatics education. http://www.qsarworld.com/cheminformatics-education.php Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./fax +44 (0)1477 533837 wendy[#]warr.com http://www.warr.com From owner-chemistry@ccl.net Mon Jan 19 09:45:01 2009 From: "Serge Dom serge.dom a gmail.com" To: CCL Subject: CCL: energy of H+ Message-Id: <-38458-090119062718-29368-CdhhrkCwzeqZgrFqLyiwUQ(0)server.ccl.net> X-Original-From: Serge Dom Content-Type: multipart/alternative; boundary=001636c5b1e4d705640460d36110 Date: Mon, 19 Jan 2009 12:28:22 +0200 MIME-Version: 1.0 Sent to CCL by: Serge Dom [serge.dom(-)gmail.com] --001636c5b1e4d705640460d36110 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello, I need to calculate the reaction where H connected to N of pyridine as a reactant and in the product I have H+ and pyridine(-). How can I calculte the energy of H+ in order to know if the reaction is exothermic or endothermic? Thank you Serge --001636c5b1e4d705640460d36110 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

Hello,

I need to calculate the reaction where H connected to N of pyridine as a reactant and in the product I have H+ and pyridine(-).

How can I calculte the energy of H+ in order to know if the reaction is exothermic or endothermic?

Thank you Serge

--001636c5b1e4d705640460d36110-- From owner-chemistry@ccl.net Mon Jan 19 11:17:01 2009 From: "Berger Raphael berger(~)chem.helsinki.fi" To: CCL Subject: CCL: energy of H+ Message-Id: <-38459-090119104902-25302-hK4wKlAncmPkAV803M7JKA~!~server.ccl.net> X-Original-From: Berger Raphael Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 19 Jan 2009 17:48:45 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Berger Raphael [berger-x-chem.helsinki.fi] Hello, I guess its just a potential, so its zero. You usually add the electronic energy (no electrons => 0) to the internuclear repulsion (the proton does not repell itself => 0), so your contribution zero unless you do want account for BSSE... best regards R. Berger ---------------------------------------------- Dr. Raphael J. F. Berger Anorganische Chemie und Strukturchemie Universitaet Bielefeld Fakultaet fuer Chemie Universitaetsstr. 25 D-33615 Bielefeld Germany Tel.: ++49-521-106 2143 Labor ++49-521-106 6164 Buero Email: raphael.berger**uni-bielefeld.de (off.) berger**chem.helsinki.fi (priv.) ---------------------------------------------- On Mon, 19 Jan 2009, Serge Dom serge.dom a gmail.com wrote: > Hello, > > I need to calculate the reaction where H connected to N of pyridine as a > reactant and in the product I have H+ and pyridine(-). > How can I calculte the energy of H+ in order to know if the reaction is > exothermic or endothermic? > > Thank you Serge > From owner-chemistry@ccl.net Mon Jan 19 13:17:01 2009 From: "Ulrike Salzner salzner++gmail.com" To: CCL Subject: CCL: energy of H+ Message-Id: <-38460-090119115810-17375-F/VE7DwBkAJoQ93iOifhDQ%a%server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 19 Jan 2009 17:53:11 +0200 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner,,gmail.com] Dear Serge, the energy of H+ is zero. There are no electrons. Ulrike On Mon, Jan 19, 2009 at 12:28 PM, Serge Dom serge.dom a gmail.com wrote: > Hello, > > I need to calculate the reaction where H connected to N of pyridine as a > reactant and in the product I have H+ and pyridine(-). > How can I calculte the energy of H+ in order to know if the reaction is > exothermic or endothermic? > > Thank you Serge -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara From owner-chemistry@ccl.net Mon Jan 19 13:51:01 2009 From: "Tobias Kraemer tobiask^_^chem.gla.ac.uk" To: CCL Subject: CCL: energy of H+ Message-Id: <-38461-090119131330-32680-nZPh83krMJWY1PEv6XWyNQ,server.ccl.net> X-Original-From: Tobias Kraemer Content-Type: multipart/alternative; boundary="------------050809050300020904030701" Date: Mon, 19 Jan 2009 16:46:24 +0000 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobiask#%#chem.gla.ac.uk] This is a multi-part message in MIME format. --------------050809050300020904030701 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello Serge... your problem is very much related to the calculation of pKA values and redox potentials. In order to calculate the Gibbs reaction energy you can use the Gibbs free energy of the proton in gasphase (at 298.15 K, 1 atm), using the Sackur-Tetrode equation to calculate the entropy part. G = H - TS = U + pV - TS = U(trans) + RT - TS = 3/2 RT + RT - TS = 5/2 RT - TS => Ggas (H+) = 5/2 RT - 7.76 kcal / mol This yields as value for Ggas(H+) of -6.28 kcal / mol Some further readings: Noodleman/ et al., Inorg. Chem./, *1996*, /35/, 4694-4702 Geerlings/ et al. Chem. Eur. J./, *2007*, /13/, 8174-8184 Chung /et al., Bull. Korean Chem. Soc./, *2005*, /26/, 585-588 Solvation can also be taken into account: Tawa /et al./, /J. Chem. Phys./, *1998*, /109/, 4852-4863 Hope that helps.... Tobi --------------050809050300020904030701 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello Serge...

your problem is very much related to the calculation of pKA values and redox potentials.
In order to calculate the Gibbs reaction energy you can use the Gibbs free energy of the proton in gasphase (at 298.15 K, 1 atm),
using the Sackur-Tetrode equation to calculate the entropy part.
G = H - TS = U + pV - TS = U(trans) + RT - TS = 3/2 RT + RT - TS = 5/2 RT - TS
=> Ggas (H+) = 5/2 RT - 7.76 kcal / mol

This yields as value for Ggas(H+) of -6.28 kcal / mol

Some further readings:

Noodleman et al., Inorg. Chem., 1996, 35, 4694-4702
Geerlings et al. Chem. Eur. J., 2007, 13, 8174-8184
Chung et al., Bull. Korean Chem. Soc., 2005, 26, 585-588

Solvation can also be taken into account:
Tawa et al., J. Chem. Phys., 1998, 109, 4852-4863

Hope that helps....

Tobi

--------------050809050300020904030701-- From owner-chemistry@ccl.net Mon Jan 19 16:56:01 2009 From: "Rene Thomsen rt(-)molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Data Modeller v2.0.0 Message-Id: <-38462-090119164636-31970-Y6BUNPTNASUpgLTgpcJGxg : server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 19 Jan 2009 16:46:32 -0500 Sent to CCL by: "Rene Thomsen" [rt||molegro.com] Aarhus, Denmark, January 19th, 2009 - Molegro is pleased to announce a new release of Molegro Data Modeller, a cross-platform application for Data Mining, Data Modelling, and Data Visualization. Molegro Data Modeller offers a high-quality modelling tool based on state-of-the-art data mining techniques combined with a user interface experience focusing on usability and productivity. The highly interactive user interface of Molegro Data Modeller is ideal for fast and intuitive data exploration, as opposed to complex workflow based solutions or command-driven statistical products. Molegro Data Modeller is available for Windows, Linux, and Mac OS X. New features in version 2.0: * Classification models: MDM now supports the following multi-class classification models: K-Nearest Neighbor and Support Vector Machines with Linear, Radial, Sigmoid, and Polynomial kernel functions. The classification models support automatic optimization of model parameters and feature selection. * Chemistry module: MDM is now able to show 2D depictions of molecules. Molecules may be imported in SDF format or as SMILES strings. Molecules may be depicted inside the spreadsheet cells or in a separate grid window. It is also possible to visualize the molecules directly in the 2D plotter and optionally cluster overlapping molecules. * A new Bivariate Analysis dialog for analyzing classification results (confusion matrix, precision / recall, F-measure, and several other measures). * A new threshold-based clustering method. * Minor user interface improvements and bug fixes (see Release Notes for details). To download a trial version, please visit our company website at: http://www.molegro.com. For more information contact: Rene Thomsen, CEO Molegro C. F. Moelles Alle, Bldg. 1110 DK-8000 Aarhus Denmark E-mail: rt###molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience.