From owner-chemistry@ccl.net Mon Jan 5 08:25:00 2009 From: "Stephen.Garrison_._srnl.doe.gov" To: CCL Subject: CCL: MOPAC/PM6 and MD Message-Id: <-38385-090105082340-7808-48I3mMBZGFFlBr2hE6JfTA%server.ccl.net> X-Original-From: Stephen.Garrison_._srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 00497D1585257535_=" Date: Mon, 5 Jan 2009 08:22:37 -0500 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison]^[srnl.doe.gov This is a multipart message in MIME format. --=_alternative 00497D1585257535_= Content-Type: text/plain; charset="US-ASCII" Are there any molecular dynamics codes that interface with MOPAC (2007 or 2009) to do MD simulations using the PM6 method? -- Stephen L. Garrison, Ph.D. Senior Engineer Engineering Modeling and Simulation Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison:SRNL.doe.gov --=_alternative 00497D1585257535_= Content-Type: text/html; charset="US-ASCII"
Are there any molecular dynamics codes that interface with MOPAC (2007 or 2009) to do MD simulations using the PM6 method?

--
Stephen L. Garrison, Ph.D.
Senior Engineer
Engineering Modeling and Simulation
Savannah River National Laboratory
Savannah River Site
773-42A, Room 181
Aiken, SC 29808
803-725-2404
Stephen.Garrison:SRNL.doe.gov
 --=_alternative 00497D1585257535_=-- From owner-chemistry@ccl.net Mon Jan 5 09:00:01 2009 From: "Berger Raphael berger,chem.helsinki.fi" To: CCL Subject: CCL: all-electron basis sets for Au; ORCA, TURBOMOLE, MOLPRO Message-Id: <-38386-090105035649-3122-YfCm06S9SKaBe9dGcYce8g^_^server.ccl.net> X-Original-From: Berger Raphael Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 5 Jan 2009 10:20:11 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Berger Raphael [berger---chem.helsinki.fi] Dear Readers, for DKH benchmark calculations on gold compounds, I try to get all-electron basis sets. While I was not able to find any but the "Ahlrichs-Coulomb-Fitting" and a "WTBS" the EMSL exchange library, ORCA switches from TZVPP to an TZV-DKH dy default on using DKHn: "WARNING: Replacing TZV by TZV-DKH" It claims the same for QZVPP: "WARNING: Replacing QZV by QZV-DKH" But in fact, both are the _same_ basis sets: Type Au : 22s15p11d6f2g contracted to 17s11p8d3f2g pattern {61111111111111111/51111111111/41111111/411/11} Moreover its stated that this set comes from the TURMOMOLE basis set library (where I can't find it). My questions now: ================= 1. Orca-related: Where does this basis exactly come from [how is it constructed, which quality is it (TZ,QZ,ATZ,...), ref. ]? 2. general: Are there "standardized" (with a sensible hierarchy) all-electron-basis sets for d- and f-Block Elements to be used with scalar relativistic computations? 3. Molpro-related: Orca prints also the respective RI-auxilliary basis set: Type Au : 25s9p9d5f4g contracted to 25s9p9d5f4g pattern {1111111111111111111111111/111111111/111111111/11111/1111} So I thought of using DF- methods and finally maybe even explicitly correlated methods (F12), but these require besides the DF_BASIS also an RI_BASIS. What could be a sensible choice for that? (Yes, my molecule is very very small :-) ) Thank You for reading and best regards R. Berger P.S. There are some related topics in the list, but I could not find one which really hits my point. From owner-chemistry@ccl.net Mon Jan 5 09:35:00 2009 From: "Jim Kress ccl_nospam{=}kressworks.com" To: CCL Subject: CCL: Any software for Protein-Ion interaction Message-Id: <-38387-090105092333-11244-NH0LBnK5uxEEXkmyJeBTqg=-=server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Jan 2009 09:20:20 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%x%kressworks.com] Gromacs Amber Charmm To name a few Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com . ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com . ccl.net] > On Behalf Of Jackie J Shen shenjiee__yahoo.com > Sent: Sunday, January 04, 2009 7:26 AM > To: Kress, Jim > Subject: CCL: Any software for Protein-Ion interaction > > > Sent to CCL by: "Jackie J Shen" [shenjiee::yahoo.com] Dear all, > > Are there any softwares for studying protein-ion > interactions? I want to know where the ions could interact > with a protein. How can I deal with this kind of problems? > > Thank you very much. > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the . sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Mon Jan 5 10:10:00 2009 From: "Jim Kress ccl_nospam*_*kressworks.com" To: CCL Subject: CCL: MOPAC/PM6 and MD Message-Id: <-38388-090105094952-31992-of3sffhPdIsWMaz14MVOrg*o*server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Jan 2009 09:36:31 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam]=[kressworks.com] Did you look at CP2K, CPMD or Quantum-expresso? How about gromacs or Charmm? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com . ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com . ccl.net] > On Behalf Of Stephen.Garrison_._srnl.doe.gov > Sent: Monday, January 05, 2009 8:23 AM > To: Kress, Jim > Subject: CCL: MOPAC/PM6 and MD > > > Are there any molecular dynamics codes that interface with > MOPAC (2007 or 2009) to do MD simulations using the PM6 method? > > -- > Stephen L. Garrison, Ph.D. > Senior Engineer > Engineering Modeling and Simulation > Savannah River National Laboratory > Savannah River Site > 773-42A, Room 181 > Aiken, SC 29808 > 803-725-2404 > Stephen.Garrison{:}SRNL.doe.gov > > From owner-chemistry@ccl.net Mon Jan 5 10:54:00 2009 From: "allouche allouche]^[lasim.univ-lyon1.fr" To: CCL Subject: CCL: MOPAC/PM6 and MD Message-Id: <-38389-090105100246-9307-cg0oOfyBIXnAFaMkwAzoQA_-_server.ccl.net> X-Original-From: allouche Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 05 Jan 2009 15:26:03 +0100 MIME-Version: 1.0 Sent to CCL by: allouche [allouche,,lasim.univ-lyon1.fr] Stephen.Garrison_._srnl.doe.gov a écrit : > > Are there any molecular dynamics codes that interface with MOPAC (2007 > or 2009) to do MD simulations using the PM6 method? The developpement version (2.1.13) of Gabedit can do this. You can download this version from : http://sites.google.com/site/allouchear/Home/gabedit/download -- Abdul-Rahman ALLOUCHE Fax : + (33) (0) 472431507 Email : allouche(a)lasim.univ-lyon1.fr Web : http://sites.google.com/site/allouchear/ From owner-chemistry@ccl.net Mon Jan 5 11:27:00 2009 From: "Frank Neese neese|,|thch.uni-bonn.de" To: CCL Subject: CCL: all-electron basis sets for Au; ORCA, TURBOMOLE, MOLPRO Message-Id: <-38390-090105105646-32163-MYMxsYSTnoVgiynjM+AIMQ{}server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 05 Jan 2009 15:56:13 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese..thch.uni-bonn.de] Dear Raphael, The ORCA basis set for gold: {61111111111111111/51111111111/41111111/411/11} comes from our paper Pantazis, D.; Chen, X.-Y.; Landis, C.R.; Neese, F. (2008) All Electron Scalar Relativistic Basis Sets for Third Row Transition Metal Atoms. J. Chem. Theor. Comp., 4, 908-919 there the entire procedure is described in detail. see also the geometry benchmarks (ECP versus scalar relativistic all electron): Bühl, M.; Reimann, C.; Pantazis, D.A.; Bredow, T.; Neese, F. (2008) Geometries of Third-row Transition-Metal Complexes from Density-Functional Theory J. Chem. Theor. Comp., 4, 1449-1459 As we describe in the paper, the connection to the TurboMole library is the following: for elements H-Xe we use the primitives from the TurboMole SV, TZV and QZV basis sets and recontracted in scalar relativistic CASSCF calculations. For third row transition metals, the primitives have been generated by us according to simple heuristic rules and contracted as specified. The polarization function exponents come from the TurboMole library and are normally used together with the standard ECP basis sets. We have done the same for lanthanides and will submit the paper soon. As far as we can see these basis sets are accurate enough for general use and denfinitely accurate enough for DFT. Hope that helps, best regards, Frank Neese -- ----------------------------------------------------------------- Prof. Dr. Frank Neese Chair of Theoretical Chemistry Department of Chemistry University of Bonn Wegelerstr. 12 D-53115 Bonn Germany E-Mail: neese*thch.uni-bonn.de URL: http://www.thch.uni-bonn.de/tc/ Telephone: +49-228-732351 ----------------------------------------------------------------- From owner-chemistry@ccl.net Mon Jan 5 12:02:00 2009 From: "Emmanuel Baribefe Naziga baribefe ~~ gmail.com" To: CCL Subject: CCL: MOPAC/PM6 and MD Message-Id: <-38391-090105092728-13828-ocJHkatGDOQhb0/7z2zEGA!A!server.ccl.net> X-Original-From: "Emmanuel Baribefe Naziga" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 5 Jan 2009 15:26:59 +0100 MIME-Version: 1.0 Sent to CCL by: "Emmanuel Baribefe Naziga" [baribefe _ gmail.com] Hello Stephen You can do MD using PM6 in cp2k (http://cp2k.berlios.de/) Emmanuel On Mon, Jan 5, 2009 at 2:22 PM, Stephen.Garrison_._srnl.doe.gov wrote: > > Are there any molecular dynamics codes that interface with MOPAC (2007 or > 2009) to do MD simulations using the PM6 method? > > -- > Stephen L. Garrison, Ph.D. > Senior Engineer > Engineering Modeling and Simulation > Savannah River National Laboratory > Savannah River Site > 773-42A, Room 181 > Aiken, SC 29808 > 803-725-2404 > Stephen.Garrison{:}SRNL.doe.gov > From owner-chemistry@ccl.net Mon Jan 5 13:04:00 2009 From: "Gerald Knizia knizia:+:theochem.uni-stuttgart.de" To: CCL Subject: CCL: all-electron basis sets for Au; ORCA, TURBOMOLE, MOLPRO Message-Id: <-38392-090105123924-24845-SILgWe0tlQOudVxlRewCAg * server.ccl.net> X-Original-From: Gerald Knizia Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 5 Jan 2009 18:03:36 +0100 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia^_^theochem.uni-stuttgart.de] On Monday 05 January 2009 09:20, Berger Raphael berger,chem.helsinki.fi wrote: > 3. Molpro-related: > Orca prints also the respective RI-auxilliary basis set: > Type Au : 25s9p9d5f4g contracted to 25s9p9d5f4g pattern > > {1111111111111111111111111/111111111/111111111/11111/1111} So I thought of > using DF- methods and finally maybe even explicitly correlated methods > (F12), but these require besides the DF_BASIS also an RI_BASIS. What could > be a sensible choice for that? 1) At this moment F12 methods in MOLPRO will not work in conjunction with ECPs or DKH Hamiltonians (currently, dipole fields are the only supported core Hamiltonian patches. In F12 methods this issue is more complicated than it looks). This will likely change in the future, but not within the next few weeks. 2) Basis sets for RI: MP2FIT basis sets from the Ahlrichs group are available for pretty much all elements, and these would probably do the trick if used as RI bases. We typically used Weigend's JKFIT basis sets for RI purposes, but if I'm not mistaken, these are only available for 1st- and 2nd-row main group elements. Kirk A. Peterson recently developed some new Optimized RI basis sets, but these are also only available for this limited set. -- Gerald Knizia From owner-chemistry@ccl.net Mon Jan 5 14:15:03 2009 From: "Tapas Kar tapaskar()cc.usu.edu" To: CCL Subject: CCL: Electronic contribution to thermal conductivity Message-Id: <-38393-090105133918-20521-X2svAH0W6FU6r2ASotQkdw-.-server.ccl.net> X-Original-From: "Tapas Kar" Date: Mon, 5 Jan 2009 13:39:14 -0500 Sent to CCL by: "Tapas Kar" [tapaskar~~cc.usu.edu] Hi, I am looking for suggestion/reference/software to theoretically estimate Electronic thermal conductivity of carbon nanotubes. Thanks Tapas From owner-chemistry@ccl.net Mon Jan 5 16:38:00 2009 From: "Egbert Zojer egbert.zojer.:.tugraz.at" To: CCL Subject: CCL: molecular mechanics and dynamics for metal-organic and organic-organic Message-Id: <-38394-090105111046-8415-/XuwdWNfG2AtSUTC08/R8A%%server.ccl.net> X-Original-From: "Egbert Zojer" Date: Mon, 5 Jan 2009 11:10:42 -0500 Sent to CCL by: "Egbert Zojer" [egbert.zojer]_[tugraz.at] Dear all, For the past few years, we have used density functional theory to describe the properties of metal organic systems. These include self-assembled monolayers on noble metals, or strong organic acceptors and donors (experiencing significant charge transfer when bonded to the metal surface) As a complementary approach (bearing in mind all the limitations of DFT, like the inability to describe dispersion forces, which to our experience only partly overcome by non-local functionals + to be able to describe much larger and more complex systems), I would like to try out approaches based on classical force fields (in particular MD). Unfortunately, I know not much about such force fields apart from their "general properties". Therefore, I would be grateful about information on force fields (+ suitable computar codes - if possible available free of charge) with a proven track-record in * describing the interaction between conjugated organic molecules, * possibly also reasonably well parametrized to describe interactions between organic molecules and noble (or not so noble) metals in the absence of metal-organic charge transfer. * codes that would also allow to include charged species (if necessary to be calculated on the DFT level. * info on shortcomings to be expected when applying such an approach that a person with only a rudimentary understanding of force fields might overlook. Thanks a lot in advance, Egbert From owner-chemistry@ccl.net Mon Jan 5 17:58:00 2009 From: "Yubo Fan yubofan*o*mail.chem.tamu.edu" To: CCL Subject: CCL: restraint for dummy atom Message-Id: <-38395-090105173506-1057-7lXsYbiiytIt9iVxJYPwiQ~!~server.ccl.net> X-Original-From: "Yubo Fan" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=gb2312;format="flowed" Date: Mon, 05 Jan 2009 15:34:40 -0600 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan .. mail.chem.tamu.edu] Hi, everyone, I am running free energy perturbation calculations with Amber 9. I know how to set a restraint between two atoms in a system. But is it possible to set a restraint between an atom and a dummy atom, which is the middle point of the CA atoms of three residues? Any advice? Thanks in advance. Yubo Fan