From owner-chemistry@ccl.net Wed May 6 02:39:01 2015 From: "Simmie, John john.simmie+/-nuigalway.ie" To: CCL Subject: CCL: Calculating transport numbers for kinetic modelling Message-Id: <-51346-150506023308-1968-7+eGSb5nZGMLSTxgrPCiXA[*]server.ccl.net> X-Original-From: "Simmie, John" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 6 May 2015 06:32:15 +0000 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie%a%nuigalway.ie] > Sent to CCL by: "Peter Kraus" [p.kraus12*imperial.ac.uk] Dear colleagues, I would like to calculate transport properties for a set of species for > application in kinetic modelling, namely the following: >Lennard-Jones sigma and epsilon, >rotational collision number (Zrot), >rotational heat capacoty (Crot), >gas phase (vapour) viscosity, Ahren Jasper (CRF, Sandia National Lab) has developed "OneDMin: A code for calculating Lennard-Jones parameters from detailed intermolecular potentials via one-dimensional minimizations" which is probably the best available method. However ultra-simple estimations using the rules in "Chemically Reacting Flow - Theory & Practice" by Kee, Coltrin & Glarborg based on molecular volumes at boiling point, etc or computed from polarisabilites as outlined by Cambi et al J Chem Phys 1991, 95, 1852 work quite well insofar as one can tell and certainly as regards chemical kinetic modelling. Prof. John M. Simmie::Combustion Chemistry Centre NUI Galway::Ireland Mo shùile togam suas From owner-chemistry@ccl.net Wed May 6 07:28:00 2015 From: "Lela Vukovic Lvukov1=illinois.edu" To: CCL Subject: CCL: Workshop on Computational Biophysics, Odense, Denmark, Oct 12-16, 2015 Message-Id: <-51347-150506024212-3335-Qi9LyZYiMyWKxDy1JdWCNg\a/server.ccl.net> X-Original-From: "Lela Vukovic" Date: Wed, 6 May 2015 02:42:09 -0400 Sent to CCL by: "Lela Vukovic" [Lvukov1(_)illinois.edu] The Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the University of Illinois at Urbana-Champaign (www.uiuc.edu), announces a "Hands-On" Workshop on Computational Biophysics http://www.ks.uiuc.edu/Training/Workshop/Odense2015/ to be held October 12-16, 2015 at the University of Southern Denmark in Odense, Denmark. Application, selection, and notification of participants is on-going through September 1, 2015. The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies, and will cover the following topics: using the biophysics software VMD and NAMD, applications of VMD and NAMD in modern research, force fields and parameterizing new molecules, simulating membrane proteins and ion channels, modeling nucleic acid systems, computational nano-bio, free energy calculations. Relevant physical concepts, mathematical techniques, and computational methods will be introduced. The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Enrollment limited to 40 participants. The workshop will be held October 12-16, 2015. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions. Course materials will be provided. The workshop is sponsored by the National Institute of General Medical Sciences (www.nigms.nih.gov), the NIH Center for Macromolecular Modeling and Bioinformatics, SDU Department of Physics, Chemistry and Pharmacy, SDU Department of Biochemistry and Molecular Biology, SDU Villum Center for Bioanalytical Sciences, SDU eScience Centre, and Lundbeck Foundation. We look forward to receiving your application! TCBG Workshop Organizers Email: workshop+odense2015::ks.uiuc.edu From owner-chemistry@ccl.net Wed May 6 08:34:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor,,fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Potential Energy Scan Message-Id: <-51348-150506054421-15817-zVUuSLa9REs/yTi0LdfGbA]_[server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Wed, 06 May 2015 11:35:49 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]*[fluor.quimica.uniovi.es] On Tue, May 05, 2015 at 05:07:48PM -0400, Safiya Ess Amer amersaf85 ~~ yahoo.com wrote: > > Sent to CCL by: "Safiya Ess Amer" [amersaf85|a|yahoo.com] > Hello, all > I have a system of H2-MgO(001) I want to find Potential Energy Surface > (PES) for this system. I am using G03 and GaussView 3.07. creating input > file with help of Gaussview > [...] > hydrogen molecule must be moved above Mg1 atom which is at origin. Can I > make variables B18, B19, and B20 scanned from 2 to 8 Angstrom by 0.1 > increments at the same time. Dear Safiya, 1) What you are asking is: 'Is there a tool already created, clean and shiny to do this task?' 2) Simple answer: Maybe, is you have money to expend? Maybe if your idea has been exploited by many people before. 3) Not so simple answer: Invert some of your time to learn an easy script language and you will be free to design any mental experiment that you can imagine. 4) The task you describe is very simple in terms of scientific programming. Any good programmer with knowledge of python, awk, or even bash can do it. 5) You can try to learn a bit by yourself or find a good sci prog nearby. 6) Sorry if this is not the answer you expected, but CCL is full of the question (1). 7) Computers are a special kind of machine. They are machines to serve our brain. Each machine requires some time to dominate it, Believe it or not. Good luck, Dr. Víctor Luaña From owner-chemistry@ccl.net Wed May 6 11:52:01 2015 From: "Jeya Vimalan jeyavimalan2k-x-gmail.com" To: CCL Subject: CCL: Spin corrector - Yamagaguchi Method Message-Id: <-51349-150506115011-6039-KO3/bP+yNiQfL1Ve8OahOQ+/-server.ccl.net> X-Original-From: Jeya Vimalan Content-Type: multipart/alternative; boundary=001a1134b38a62a8a405156bbf09 Date: Wed, 6 May 2015 11:50:00 -0400 MIME-Version: 1.0 Sent to CCL by: Jeya Vimalan [jeyavimalan2k~!~gmail.com] --001a1134b38a62a8a405156bbf09 Content-Type: text/plain; charset=UTF-8 Dear all, Could anyone guide me in understanding how one can correct spin contamination based on yamagaguchi method. your help is appreciated. vimal --001a1134b38a62a8a405156bbf09 Content-Type: text/html; charset=UTF-8
Dear all,

Could anyone guide me in understanding how one can
correct spin contamination based on yamagaguchi method.

your help is appreciated.

vimal
--001a1134b38a62a8a405156bbf09-- From owner-chemistry@ccl.net Wed May 6 12:26:00 2015 From: "Asheesh Kumar akdap235!A!gmail.com" To: CCL Subject: CCL:G: keywords for interaction energy in gaussian Message-Id: <-51350-150506074011-23421-XkkOlPTZ+h6zRGy445xk4g+*+server.ccl.net> X-Original-From: "Asheesh Kumar" Date: Wed, 6 May 2015 07:40:10 -0400 Sent to CCL by: "Asheesh Kumar" [akdap235(!)gmail.com] To kindly tell the keywords for interaction energy in gaussian 09W with M06-2X 6311++G** From owner-chemistry@ccl.net Wed May 6 15:07:01 2015 From: "Mehboob Alam mehboob.cu/a\gmail.com" To: CCL Subject: CCL:G: Potential Energy Scan Message-Id: <-51351-150506122708-22917-QofQim3UPIZjXOW0WqDedw[#]server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=001a11349500d0430505156c4379 Date: Wed, 6 May 2015 18:27:01 +0200 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu]-[gmail.com] --001a11349500d0430505156c4379 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Safiya, Yes, you can do this. Please have a look at the Gaussian website - http://www.gaussian.com/g_tech/g_ur/k_scan.htm There is a nice example of multiple dimensional scan. Hope it helps Best Wishes, Mehboob Dr. Md. Mehboob Alam Post-Doctoral Researcher Institut de Chimie de Strasbourg Laboratoire de Chimie Quantique Universit=E9 de Strasbourg PostDoc Supervisor - Dr. Emmanuel Fromager On Tue, May 5, 2015 at 11:07 PM, Safiya Ess Amer amersaf85 ~~ yahoo.com < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: "Safiya Ess Amer" [amersaf85|a|yahoo.com] > Hello, all > I have a system of H2-MgO(001) I want to find Potential Energy Surface > (PES) for this system. I am using G03 and GaussView 3.07. creating input > file with help of Gaussview > > #p B3LYP 6-31G(d) popt=3Dz-matrix > > Theta=3D0 / H2-MgO > > 0 1 > > Mg > Mg 1 B1 > Mg 1 B2 A1 > Mg 3 B3 1 A2 2 D1 > Mg 1 B4 3 A3 2 D2 > Mg 4 B5 3 A4 1 D3 > Mg 5 B6 1 A5 3 D4 > Mg 1 B7 5 A6 7 D5 > Mg 8 B8 1 A7 5 D6 > O 2 B9 1 A8 5 D7 > O 4 B10 3 A9 1 D8 > O 4 B11 3 A10 1 D9 > O 3 B12 1 A11 5 D10 > O 4 B13 3 A12 1 D11 > O 4 B14 3 A13 1 D12 > O 1 B15 13 A14 3 D13 > O 6 B16 4 A15 3 D14 > O 6 B17 4 A16 3 D15 > X 1 B18 16 A17 5 D16 > H 1 B19 16 A18 5 D17 > H 1 B20 16 A19 5 D18 > > B1 4.20021428 f > B2 2.97000000 f > B3 2.97000000 f > B4 2.97000000 f > B5 2.97000000 f > B6 2.97000000 f > B7 2.97000000 f > B8 2.97000000 f > B9 2.10010714 f > B10 2.10010714 f > B11 2.10010714 f > B12 2.10010714 f > B13 2.10010714 f > B14 2.10010714 f > B15 2.10010714 f > B16 2.10010714 f > B17 2.10010714 f > B18 2.00000000 S 1 0.1 > B19 2.37000000 S 1 0.1 > B20 1.63000000 S 1 0.1 > A1 45.00000000 f > A2 90.00000000 f > A3 90.00000000 f > A4 90.00000000 f > A5 90.00000000 f > A6 90.00000000 f > A7 90.00000000 f > A8 90.00000000 f > A9 45.00000000 f > A10 135.00000000 f > A11 45.00000000 f > A12 45.00000000 f > A13 135.00000000 f > A14 90.00000000 f > A15 135.00000000 f > A16 135.00000000 f > A17 90.00000000 f > A18 90.00000000 f > A19 90.00000000 f > D1 180.00000000 f > D2 0.00000000 f > D3 0.00000000 f > D4 180.00000000 f > D5 0.00000000 f > D6 180.00000000 f > D7 180.00000000 f > D8 180.00000000 f > D9 180.00000000 f > D10 0.00000000 f > D11 0.00000000 f > D12 0.00000000 f > D13 180.00000000 f > D14 0.00000000 f > D15 180.00000000 f > D16 90.00000000 f > D17 90.00000000 f > D18 90.00000000 f > > ********************************************* > hydrogen molecule must be moved above Mg1 atom which is at origin. Can I > make variables B18, B19, and B20 scanned from 2 to 8 Angstrom by 0.1 > increments at the same time. > > Thanks in advance > > Safiya Amer > amersas85|a|yahoo.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11349500d0430505156c4379 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Safiya,

Yes, you can do this. Please= have a look at the Gaussian website -=A0http://www.gaussian.com/g_tech/g_ur/k_scan.htm=
There is a nice example of multiple dimensional scan.
= Hope it helps

Best Wishes,
Mehboob
=

Dr. Md. Mehboob Alam<= br>
Post-Doctoral Researcher
Institut de Chimie de Strasbourg=
Laboratoire de Chimie Quantique
Universit=E9 de Strasbo= urg
PostDoc Supervisor - Dr. Emmanuel Fromager

On Tue, May 5, 2015 at 11:07 PM, Safiya Ess = Amer amersaf85 ~~ yahoo.com <owner-= chemistry(-)ccl.net> wrote:
<= br> Sent to CCL by: "Safiya Ess Amer" [amersaf85|a|yahoo.com]
Hello, all
=A0I have a system of H2-MgO(001) I want to find Potential Energy Surface (PES) for this system. I am using G03 and GaussView 3.07. creating input file with help of Gaussview

#p B3LYP 6-31G(d)=A0 popt=3Dz-matrix

Theta=3D0 / H2-MgO

0 1

=A0Mg
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01=A0 =A0 =A0 =A0 =A0 =A0 =A0 B1
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01=A0 =A0 =A0 =A0 =A0 =A0 =A0 B2=A0 = =A0 =A0 =A0 =A0 A1
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A03=A0 =A0 =A0 =A0 =A0 =A0 =A0 B3=A0 = =A0 1=A0 =A0 =A0A2=A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 D1
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01=A0 =A0 =A0 =A0 =A0 =A0 =A0 B4=A0 = =A0 3=A0 =A0 =A0A3=A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 D2
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A04=A0 =A0 =A0 =A0 =A0 =A0 =A0 B5=A0 = =A0 3=A0 =A0 =A0A4=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 D3
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A05=A0 =A0 =A0 =A0 =A0 =A0 =A0 B6=A0 = =A0 1=A0 =A0 =A0A5=A0 =A0 3=A0 =A0 =A0 =A0 =A0 =A0 =A0 D4
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01=A0 =A0 =A0 =A0 =A0 =A0 =A0 B7=A0 = =A0 5=A0 =A0 =A0A6=A0 =A0 7=A0 =A0 =A0 =A0 =A0 =A0 =A0 D5
=A0Mg=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A08=A0 =A0 =A0 =A0 =A0 =A0 =A0 B8=A0 = =A0 1=A0 =A0 =A0A7=A0 =A0 5=A0 =A0 =A0 =A0 =A0 =A0 =A0 D6
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 B9=A0 = =A0 1=A0 =A0 =A0A8=A0 =A0 5=A0 =A0 =A0 =A0 =A0 =A0 =A0 D7
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4=A0 =A0 =A0 =A0 =A0 =A0 =A0B10=A0 = =A0 3=A0 =A0 =A0A9=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 D8
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4=A0 =A0 =A0 =A0 =A0 =A0 =A0B11=A0 = =A0 3=A0 =A0 =A0A10=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0D9
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3=A0 =A0 =A0 =A0 =A0 =A0 =A0B12=A0 = =A0 1=A0 =A0 =A0A11=A0 =A0 5=A0 =A0 =A0 =A0 =A0 =A0 =A0D10
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4=A0 =A0 =A0 =A0 =A0 =A0 =A0B13=A0 = =A0 3=A0 =A0 =A0A12=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0D11
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4=A0 =A0 =A0 =A0 =A0 =A0 =A0B14=A0 = =A0 3=A0 =A0 =A0A13=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0D12
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0B15=A0 = =A013=A0 =A0 =A0A14=A0 =A0 3=A0 =A0 =A0 =A0 =A0 =A0 =A0D13
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6=A0 =A0 =A0 =A0 =A0 =A0 =A0B16=A0 = =A0 4=A0 =A0 =A0A15=A0 =A0 3=A0 =A0 =A0 =A0 =A0 =A0 =A0D14
=A0O=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6=A0 =A0 =A0 =A0 =A0 =A0 =A0B17=A0 = =A0 4=A0 =A0 =A0A16=A0 =A0 3=A0 =A0 =A0 =A0 =A0 =A0 =A0D15
=A0X=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0B18=A0 = =A016=A0 =A0 =A0A17=A0 =A0 5=A0 =A0 =A0 =A0 =A0 =A0 =A0D16
=A0H=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0B19=A0 = =A016=A0 =A0 =A0A18=A0 =A0 5=A0 =A0 =A0 =A0 =A0 =A0 =A0D17
=A0H=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0B20=A0 = =A016=A0 =A0 =A0A19=A0 =A0 5=A0 =A0 =A0 =A0 =A0 =A0 =A0D18

=A0 =A0B1=A0 =A0 =A0 =A0 =A0 =A0 =A04.20021428 f
=A0 =A0B2=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B3=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B4=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B5=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B6=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B7=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B8=A0 =A0 =A0 =A0 =A0 =A0 =A02.97000000 f
=A0 =A0B9=A0 =A0 =A0 =A0 =A0 =A0 =A02.10010714 f
=A0 =A0B10=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B11=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B12=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B13=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B14=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B15=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B16=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B17=A0 =A0 =A0 =A0 =A0 =A0 2.10010714 f
=A0 =A0B18=A0 =A0 =A0 =A0 =A0 =A0 2.00000000 S 1 0.1
=A0 =A0B19=A0 =A0 =A0 =A0 =A0 =A0 2.37000000 S 1 0.1
=A0 =A0B20=A0 =A0 =A0 =A0 =A0 =A0 1.63000000 S 1 0.1
=A0 =A0A1=A0 =A0 =A0 =A0 =A0 =A0 45.00000000 f
=A0 =A0A2=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A3=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A4=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A5=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A6=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A7=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A8=A0 =A0 =A0 =A0 =A0 =A0 90.00000000 f
=A0 =A0A9=A0 =A0 =A0 =A0 =A0 =A0 45.00000000 f
=A0 =A0A10=A0 =A0 =A0 =A0 =A0 135.00000000 f
=A0 =A0A11=A0 =A0 =A0 =A0 =A0 =A045.00000000 f
=A0 =A0A12=A0 =A0 =A0 =A0 =A0 =A045.00000000 f
=A0 =A0A13=A0 =A0 =A0 =A0 =A0 135.00000000 f
=A0 =A0A14=A0 =A0 =A0 =A0 =A0 =A090.00000000 f
=A0 =A0A15=A0 =A0 =A0 =A0 =A0 135.00000000 f
=A0 =A0A16=A0 =A0 =A0 =A0 =A0 135.00000000 f
=A0 =A0A17=A0 =A0 =A0 =A0 =A0 =A090.00000000 f
=A0 =A0A18=A0 =A0 =A0 =A0 =A0 =A090.00000000 f
=A0 =A0A19=A0 =A0 =A0 =A0 =A0 =A090.00000000 f
=A0 =A0D1=A0 =A0 =A0 =A0 =A0 =A0180.00000000 f
=A0 =A0D2=A0 =A0 =A0 =A0 =A0 =A0 =A00.00000000 f
=A0 =A0D3=A0 =A0 =A0 =A0 =A0 =A0 =A00.00000000 f
=A0 =A0D4=A0 =A0 =A0 =A0 =A0 =A0180.00000000 f
=A0 =A0D5=A0 =A0 =A0 =A0 =A0 =A0 =A00.00000000 f
=A0 =A0D6=A0 =A0 =A0 =A0 =A0 =A0180.00000000 f
=A0 =A0D7=A0 =A0 =A0 =A0 =A0 =A0180.00000000 f
=A0 =A0D8=A0 =A0 =A0 =A0 =A0 =A0180.00000000 f
=A0 =A0D9=A0 =A0 =A0 =A0 =A0 =A0180.00000000 f
=A0 =A0D10=A0 =A0 =A0 =A0 =A0 =A0 0.00000000 f
=A0 =A0D11=A0 =A0 =A0 =A0 =A0 =A0 0.00000000 f
=A0 =A0D12=A0 =A0 =A0 =A0 =A0 =A0 0.00000000 f
=A0 =A0D13=A0 =A0 =A0 =A0 =A0 180.00000000 f
=A0 =A0D14=A0 =A0 =A0 =A0 =A0 =A0 0.00000000 f
=A0 =A0D15=A0 =A0 =A0 =A0 =A0 180.00000000 f
=A0 =A0D16=A0 =A0 =A0 =A0 =A0 =A090.00000000 f
=A0 =A0D17=A0 =A0 =A0 =A0 =A0 =A090.00000000 f
=A0 =A0D18=A0 =A0 =A0 =A0 =A0 =A090.00000000 f

*********************************************
=A0hydrogen molecule must be moved above Mg1 atom which is at origin. Can I=
make variables B18, B19, and B20=A0 scanned from 2 to 8 Angstrom by 0.1
increments at the same time.

Thanks in advance

Safiya Amer
amersas85|a|yahoo.com


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--001a11349500d0430505156c4379-- From owner-chemistry@ccl.net Wed May 6 15:46:01 2015 From: "conor douglas parks coparks2012|-|gmail.com" To: CCL Subject: CCL: using stochastic thermostats in the presence of electromagnetic fields Message-Id: <-51352-150506153843-6709-/lDrst3lzlxiFqAbi187MQ-.-server.ccl.net> X-Original-From: "conor douglas parks" Date: Wed, 6 May 2015 15:38:42 -0400 Sent to CCL by: "conor douglas parks" [coparks2012*gmail.com] Hello, I am interested in phase changes in the presence of electromagnetic fields. When simulating nucleation from a metastable liquid, we get lucky and the rules of equilibrium statistical mechanics apply. Thus, I don't see any issue with applying an andersen or langevin thermostat to a system. However, I was wondering if anyone could shed light for me on the case of when an electric field is present. This is clearly a highly non equilibrium case. However, I see people in the literature applying langevin and andersen thermostats. I realize these thermostats are interactions with a fictitious bath. However, the langevin thermostat relies on the fluctuation dissipation theorem which more than likely doesn't hold for highly non equilibrium systems. Furthermore, both the langevin and andersen thermostat force a maxwellian distribution of velocities which I am not sure holds here. Is temperature even well defined in this case? Can anyone tell me if I am being overly skeptical, or if there is a safer method for thermostatting? From owner-chemistry@ccl.net Wed May 6 18:29:00 2015 From: "Jorge H Rodriguez jhrodrig^^purdue.edu" To: CCL Subject: CCL: Spin corrector - Yamagaguchi Method Message-Id: <-51353-150506182701-32403-TETc0Zhl+ZDJeYPTyxbngw^-^server.ccl.net> X-Original-From: "Jorge H Rodriguez" Date: Wed, 6 May 2015 18:27:00 -0400 Sent to CCL by: "Jorge H Rodriguez" [jhrodrig|-|purdue.edu] Dear Vimal: Please take a look at the JCP paper by J.H. Rodriguez and J.K. McCusker [J. Chem. Phys. Volume 116, Pg. 6253 (2002)]. The final Appendix of the paper contains a brief outline/derivation of Yamaguchi's spin-projection method. Perhaps this may be helpful for you. Best Regards, Jorge H. Rodriguez Purdue University > "Jeya Vimalan jeyavimalan2k-x-gmail.com" wrote: > > Sent to CCL by: Jeya Vimalan [jeyavimalan2k~!~gmail.com] > --001a1134b38a62a8a405156bbf09 > Content-Type: text/plain; charset=UTF-8 > > Dear all, > > Could anyone guide me in understanding how one can > correct spin contamination based on yamagaguchi method. > > your help is appreciated. > > vimal > > --001a1134b38a62a8a405156bbf09 > Content-Type: text/html; charset=UTF-8 > >
Dear all,

Could anyone guide me in understanding how one can
correct spin contamination based on yamagaguchi method.

your help is appreciated.

vimal
> > --001a1134b38a62a8a405156bbf09-- > >