From mattacf@mcmail.CIS.McMaster.CA Tue Jun 30 02:47:47 1998 Received: from mcmail.CIS.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.20.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA01005 Tue, 30 Jun 1998 02:47:47 -0400 (EDT) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.8/8.8.8) with SMTP id CAA22476 for ; Tue, 30 Jun 1998 02:47:31 -0400 (EDT) Date: Tue, 30 Jun 1998 02:47:31 -0400 (EDT) From: "C.F. Matta" To: chemistry@www.ccl.net Subject: Problem with Gaussian Scan Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I am trying to perform a potential energy surface scan using Gaussian94. It is the first time I try this option and the manual is not very clear as to how should one handle the following situation: 1. I optimized the z-matrix keeping three torsion angles as constants (froozen). 2. I want to use the optimized geometry from the check point file as an input to the potential energy scan BUT would like to keep ONE of the previously frozen torsions as it is, while perform the PES on the TWO others. Below, please find my input (com) file and the error message I get in my (log) file. INPUT (COM) FILE # rhf/3-21g scan opt=(AddRedundant, readfc) scf=direct scf=tight geom=modify geom=(noangle, nodistance) Diacetyl glycoluril model (with demethylated Nitrogens), June 1998. 0 1 tor5 180.0 11 30.0 tor17 180.0 11 30.0 ERROR MESSAGE IN THE LOG FILE ---------------------------------------------------------------------- # rhf/3-21g* scan opt=(AddRedundant, readfc) scf=direct 6d scf=tight g eom=modify geom=(noangle, nodistance) ---------------------------------------------------------------------- Unrecognized IType=10. Error termination via Lnk1e in /usr/people/gauss/g94/l1.exe. Job cpu time: 0 days 0 hours 0 minutes 0.6 seconds. File lengths (MBytes): RWF= 44 Int= 0 D2E= 0 Chk= 5 Scr= 1 I would much appreciate your help, and will summarize for future reference. Thank you very much, and have a good day. Cherif Matta Graduate student Chemistry Dept. McMaster University Hamilton, Ontario Canada L8S 4M1 From arthur@csb0.IPC.PKU.EDU.CN Tue Jun 30 03:07:54 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA01233 Tue, 30 Jun 1998 03:07:38 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA06504; Tue, 30 Jun 98 15:06:11 -0700 Date: Tue, 30 Jun 1998 15:06:11 -0700 (PDT) From: Arthur Wang To: CCL mailing list Subject: True or false: a simple assumption of solvation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Let's think about this: Is there a linear relationship between the solvation energies when using two different solvents? That is: if the solvation energies of molecule A in two different solvents are G(A1) and G(A2) respectively, molecule A (vaccum) ---> molecule A (solvent 1) G(A1) molecule A (vaccum) ---> molecule A (solvent 2) G(A2) there will be G(A1) = k(A)*G(A2). And, if the solvation energies of another molecule B in these two solvents are G(B1) and G(B2) respectively, molecule B (vaccum) ---> molecule B (solvent 1) G(B1) molecule B (vaccum) ---> molecule B (solvent 2) G(B2) there will be G(B1) = k(B)*G(B2). So here is the question: Does k(A) equal to k(B)? I know the answer must be: NOT ALWAYS. But I just want to know under what condition this assumption holds and under what condition it does not. Any comment? Or you can suggest me some references to read. Best wishes, Arthur Peking University, Beijing arthur@ipc.pku.edu.cn From konietz@chemie.uni-kl.de Tue Jun 30 10:06:05 1998 Received: from news.uni-kl.de (mmdf@news.uni-kl.de [131.246.137.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA03633 Tue, 30 Jun 1998 10:06:02 -0400 (EDT) Received: from iris1.chemie.uni-kl.de ( iris1.chemie.uni-kl.de [131.246.9.107] ) by news.uni-kl.de id aa15805 for ; 30 Jun 98 09:06 CDT Received: from oktarin by iris1.chemie.uni-kl.de via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id QAA17865; Tue, 30 Jun 1998 16:05:48 +0200 Received: from localhost by oktarin with smtp (Smail3.1.28.1 #7) id m0yr12a-0000ALC; Tue, 30 Jun 98 16:05 CETDST Date: Tue, 30 Jun 1998 16:05:48 +0200 (CETDST) From: Stefan Konietzny To: "Comp. Chem. List" Subject: gauopt tool in GAUSSIAN94 ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there. Is it true that a so called "gauopt"-tool is available in GAUSSIAN94 that can be used optimize basis sets. If yes, does anybody know how it works? I would like to optimize some d-polarisation functions for pseudo potential basis sets for the main group elements. Stefan. **** reply to: konietz@chemie.uni-kl.de Stefan Konietzny Dept. of Chemistry University of Kaiserslautern From elewars@alchemy.chem.utoronto.ca Tue Jun 30 13:03:05 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05521 Tue, 30 Jun 1998 13:03:04 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id NAA13079 for chemistry@www.ccl.net; Tue, 30 Jun 1998 13:03:03 -0400 (EDT) Date: Tue, 30 Jun 1998 13:03:03 -0400 (EDT) From: "E. Lewars" Message-Id: <199806301703.NAA13079@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SUMMARY OF REPLIES TO 3-21G vs. 6-31G* QUESTION 1998 June 31 Here are the replies I got to my question about the 3-21G basis vs. the 6-31G*. Thanks very much to cory@chem.ucalgary, Frank Jensen, Alan Shusterman, and German Sastre Nava. Question: > Mon, 1998 June 22 > > Hello, > > The 3-21G (strictly, 3-21G*) basis set gives geometries which are actually a > bit better than those from the 6-31G* set (Hehre, "Practical Strategies for > Electronic Structure Calculations", p 23; Hehre, Radom, Schleyer and Pople, > "Ab Initio Molecular Orbital Theory", pp 175 and 185; this is for HF-level > calculations; for correlated-level work one needs at least 6-31G*, of course). > HF/3-21G* geometries are even used for Petersson's high-accuracy CBS-4 method. > > So why (judging by the literature) is the 6-31G* basis usually preferred for > HF-level geometries? Is it because of an unexamined belief that bigger is line 1 [h for help]> better? Or is it because *relative energies* are better at the HF/6-31G* leve l > than at the HF/3-21G level? If this is the reason, then in those cases where >*both* HF and MP2 (or other correlated) calculations are reported, would it not > be better to do the HF calculations using 3-21G optimizations (then use MP2/ > 6-31G* or bigger for the post-HF jobs)? > E. Lewars ======================= REPLIES #1 Cory Date: Mon, 22 Jun 1998 18:43:30 -0600 To: elewars@alchemy.chem.utoronto.ca Subject: 3-21G* vs 6-31G* One of the reasons that 6-31G* is preferred over 3-21G* is that, strictly speaki ng, 3-21G* does not use polarization functions on 'first-row' atoms C,N,O,F. This is a big problem for things like amines, where generally the amine is too flat (pyramidality is underestimated). We have noticed a similar thing with R3O+ species (protonated benzene oxide, JPC A, 1997, 3371), but I'm sure that this must have been noticed before. Another problem is that cationic-metal to oxygen distances are a little too short (JPC, 1995, 3793 - 3-21G = 1.89, 6-31G* = 1.97, Expt = 1.96). This is a problem with the valence region, since in other systems 6-21G ~ 3-21G, and not with the core, as we initially thought. -Cory ============= #2 Frank Jensen Jun 23 Frank Jensen (66) Re: CCL:3-21G vs. 6-31G(d) geom optCommand: Read MessageMessage 2/5 from Frank Jensen Jun 23 '98 at 7:51 am Date: Tue, 23 Jun 1998 07:51:40 +0200 (METDST) To: "E. Lewars" Subject: Re: CCL:3-21G vs. 6-31G(d) geom opt Message-ID: MIME-Version: 1.0 At the HF level, bigger basis means converging toward the HF limit. This has some known deficiencies, like all (covalent) bonds being too short. Using a smaller basis gives longer bond lengths, and 3-21G(*) may be some sort of "Pauling" point, where some "magic" cancellation of errors occurs. I would consider the 3-21G as being too small in the core region, and results may in some case be unpredictable, i.e. the average error may be better than 6-31G*, but the maximum deviation may be larger. The 6-31G* should give more uniform results, but they have a systematic error. Using the same basis for HF and MP2 gives you a chance of evaluating the correlation effect, independent of the basis set effect. One could probably come up with an empirical scheme for adding corrections to the HF/6-31G* results give give better answers than HF/3-21G(*), but then again DFT would probably beat that any day... And yes, relative energies would certainly be better with the 6-31G*, but again subject to systematic errors. Frank ============= #3 Alan Shusterman Jun 22 Alan Shusterman (42) Re: CCL:3-21G vs. 6-31G(d) geom optCommand: Read MessageMessage 3/5 from Alan Shusterman Jun 22 '98 at 11:27 pm Message-id: <5826880@isis.reed.edu> Date: 22 Jun 98 23:27:10 PDT Subject: Re: CCL:3-21G vs. 6-31G(d) geom opt To: elewars@alchemy.chem.utoronto.ca --- You wrote: The 3-21G (strictly, 3-21G*) basis set gives geometries which are actually a bit better than those from the 6-31G* set (Hehre, "Practical Strategies for Electronic Structure Calculations", p 23; --- end of quote --- I've read p 23, but I can't find a statement saying 3-21G* is "a bit better" than 6-31G*. There certainly are examples in the tables where 3-21G(*) performs better, but there are counter-examples too (and a statistical analysis, assuming a fair one is possible, might show that 6-31G* errors are, on average, smaller). Another thing to keep in mind is that bond distances are only one aspect of molecular geometry. The statement on p. 23 makes no mention of bond angles, dihedral angles, and so on. 3-21G* is not very effective at certain problems, such as amine bond angles. These objections do not get at your real question, however, which is "why should one do the extra work associated with a larger basis set?" (Larger, by the way, only in regard to Gaussian primitives; the number of contracted functions in 3-21G* and 6-31G* are the same.) 3-21G* geometries should be satisfactory in most cases. Alan --------------- Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan ========== #4 German Sastre Nava Jun 23 German Sastre Nava (48) Re: CCL:3-21G vs. 6-31G(d) geom optCommand: Read MessageMessage 4/5 from German Sastre Navarro Jun 23 '98 at 4:18 am Subject: Re: CCL:3-21G vs. 6-31G(d) geom opt To: elewars@alchemy.chem.utoronto.ca (E. Lewars) Date: Tue, 23 Jun 1998 04:18:17 -0400 (EDT) Hi, > So why (judging by the literature) is the 6-31G* basis usually preferred for > HF-level geometries? Is it because of an unexamined belief that bigger is > better? Or is it because *relative energies* are better at the HF/6-31G* leve l > than at the HF/3-21G level? In the kind of reactions I'm used to work in (adsorption of organic mol. over alumino-silicates) this is indeed the case. 3-21g* tends to overestimate adsorption energies and also activation energies. Apart from that, another minor problem seems to be the relatively high atomic charge separation in 3-21g*. > If this is the reason, then in those cases where >*both* HF and MP2 (or other correlated) calculations are reported, would it not t > be better to do the HF calculations using 3-21G optimizations (then use MP2/ > 6-31G* or bigger for the post-HF jobs)? I very much agree. I hope the rest of the CCL can also give their view over this interesting question. Regards German \|/ (o o) ------------------------------------------oOO-(_)-OOo----------------------- German Sastre URL: http://www.ri.ac.uk/DFRL/G.Sastre Instituto de Tecnologia Quimica e-mail: gsastre@itq.upv.es Universidad Politecnica de Valencia Phone: +34 (9)6-387-7803 Av. Los Naranjos s/n. 46022 Valencia (Spain) Fax: +34 (9)6-387-7809 ---------------------------------------------------------------------------- oo0 0oo ================ From elewars@alchemy.chem.utoronto.ca Tue Jun 30 13:10:44 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05608 Tue, 30 Jun 1998 13:10:43 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id NAA13251 for chemistry@www.ccl.net; Tue, 30 Jun 1998 13:10:43 -0400 (EDT) Date: Tue, 30 Jun 1998 13:10:43 -0400 (EDT) From: "E. Lewars" Message-Id: <199806301710.NAA13251@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: REF REQUESTED TO PAPER ON NOBLE GAS CHEMISTRY 1998 June 31 Hello, has anyone the full reference to this paper (book chaper?)-- journal or book, year, vol, publisher etc: "The Chemistry of the Noble Gas Elements Helium, Neon, and Argon-Experimental Facts and Theoretical Predictions" Gernot Frenking and Dieter Cremer (year about 1990) Thanks E. Lewars =============== From johns@ks.uiuc.edu Tue Jun 30 13:53:28 1998 Received: from london.ks.uiuc.edu (london.ks.uiuc.edu [128.174.214.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05938 Tue, 30 Jun 1998 13:53:27 -0400 (EDT) Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2) id AA273489208; Tue, 30 Jun 1998 12:53:28 -0500 Received: (from johns@localhost) by bilbao.ks.uiuc.edu (951211.SGI.8.6.12.PATCH1502/8.6.9)id MAA28647 for chemistry@www.ccl.net; Tue, 30 Jun 1998 12:53:27 -0500 From: John Stone Message-Id: <199806301753.MAA28647@bilbao.ks.uiuc.edu> Subject: VMD (Visual Molecular Dynamics) 1.2b3 Available To: chemistry@www.ccl.net Date: Tue, 30 Jun 1998 12:53:27 -0500 (CDT) X-Mailer: ELM [version 2.4ME+ PL14 (25)] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Announcing version 1.2b3 release of VMD --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability of version 1.2b3 of the program VMD, a package for the vizualization and analysis of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and precompiled binaries for SGIs, HPs, Solaris 2, and Linux. The documentation (still being updated) includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ New in this version ------------------- o VMD now supports AIX 4.x with the native AIX OpenGL implementation o OpenGL rendering speed has been improved by 2-5x on several platforms o OpenGL version now correctly supports stereo-in-a-window o OpenGL/GL versions are now able to interoperate with VMD scripts created in by one or the other. o Upgraded some builds to use newer XForms libraries, which fix some GUI/Mouse bugs o VMD upgraded to compile with the 2.6c release of the CAVE libraries o VMD code now builds with much pickier C++ compilers (i.e. HP aCC) o New Linux binary distributions have working file browser now. o New Linux RPM style binary distribution o New HPUX10-OpenGL binaries for Visualize-FX hardware accelerators o New AIX4-OpenGL binaries for IBM OpenGL hardware accelerators o Many bug fixes Version 1.2b2 features ---------------------- o VMD has been ported to Sun Solaris 2. o Upgraded to support Linux RedHat 5.0 o OpenGL support works with native HP-UX and Sun OpenGL implementations o Added Tk support and upraded to Tcl/Tk 8.0 o Upgraded to Babel 1.6 o Added support for MSMS, a program for calculating molecular surfaces o Added support for Grasp file format o For most commands, typing in a command without arguments will print a help message o Added more commands to Tcl scripting interface o Many bug fixes Version 1.2b1 features ---------------------- o This biggest improvement in version 1.2b1 support for platforms other than GL-based SGIs. In addition to the full source and SGI binary distributions, VMD is now available for HP-UX (tested under 9 and 10) and Linux. o Greatly enhanced Tcl scripting commands for performing molecular analysis, writing scripts, developing tutorials, etc. o New rendering styles, a fast (and cheap) solvent accessible surface and C-alpha and P trace method, and improvements to the existing styles. o New output renderer formats: Postscript, VRML and STL (a stereo-lithography format) o Support for Amber structure and animation file formats ============= Basic information about VMD ================= Features -------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o No limits on the number of molecules, atoms, residues or number of animation frames, excepting available memory. o Many molecular rendering and coloring methods. o Stereo display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Radiance. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis o Modular, extensible source code using an object-oriented design in C++, with a programmer's guide describing the source code o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd/ VMD can be used to set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment. Availability ------------ The software is available for downloading from http://www.ks.uiuc.edu/Research/vmd/ Please email any questions to vmd@ks.uiuc.edu. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. For more information, see http://www.ks.uiuc.edu/Research/MDScope/. This project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969) and the Roy J. Carver Charitable Trust. John Stone vmd@ks.uiuc.edu June 25, 1998 -- Theoretical Biophysics Group Email: johns@ks.uiuc.edu Beckman Institute http://www.ks.uiuc.edu/~johns/ University of Illinois Phone: (217) 244-3349 405 N. Mathews Ave FAX: (217) 244-6078 Urbana, IL 61801, USA Unix Is Good For You!!! From ijbarani@syr.edu Tue Jun 30 13:54:20 1998 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.1.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05961 Tue, 30 Jun 1998 13:54:19 -0400 (EDT) Received: from syr.edu (casehead.cat.syr.edu [128.230.59.14]) by mailbox.syr.edu (8.9.0/8.9.0) with ESMTP id NAA08257 for ; Tue, 30 Jun 1998 13:54:21 -0400 (EDT) Message-ID: <3599259E.68F9225@syr.edu> Date: Tue, 30 Jun 1998 13:51:26 -0400 From: "Igor J. Barani" X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Summary: MM3/MM2 Input files References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to thank all those who responded to my information request concerning MM2/MM3 input files. I think that the general consensus was that BABEL which is available from http://mercury.aichem.arizona.edu/babel.html is the most versatile program for generating such files. Thank you. Sincerely, Igor Barani From jaimeco@U.Arizona.EDU Tue Jun 30 15:06:17 1998 Received: from f1n4.u.arizona.edu (f1n4.U.Arizona.EDU [128.196.137.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA07108 Tue, 30 Jun 1998 15:06:17 -0400 (EDT) Received: from localhost (jaimeco@localhost) by f1n4.u.arizona.edu (8.8.8/8.8.8) with SMTP id MAA41084; Tue, 30 Jun 1998 12:06:07 -0700 Date: Tue, 30 Jun 1998 12:06:06 -0700 (MST) From: Jaime Combariza Reply-To: Jaime Combariza To: Stefan Konietzny cc: "Comp. Chem. List" Subject: Re: CCL:G:gauopt tool in GAUSSIAN94 ? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII here is an exmaple I used to optimize the basis functions for an F anion: (The results are close but not exactly the same as those obtained using GAMESS and the option trudge). Notice the first two lines and the format. 4 20 T 0.0 0.0 0.10760000V 7.0 V 1.75 V 0.4375 V #p rhf/gen 6d test scf=direct F- Optimize last 4 basis functions -1 1 f 1 0 s 6 1.0 11427.100000 .001801 1722.350000 .013742 395.746000 .068133 115.139000 .233325 33.602600 .589086 4.919010 .299505 SP 3 1.0 55.444100 .114536 .035461 12.632300 .920512 .237451 3.717560 -.003378 .820458 SP 1 1.0 1.165450 1.00000 1.00000 SP 1 1.0 .321892 1.00000 1.00000 SP 1 1.0 <1 12.10> 1.00000 1.00000 D 1 1.0 <2 12.10> 1.00000 D 1 1.0 <3 12.10> 1.00000 D 1 1.0 <4 12.10> 1.000000 **** Then you will run this as: ($path)/gauopt < input_file > output_file gauopt is a link to g94opt. gauopt calls g94 to run the energy calculations. Jaime E. Combariza jaimeco@pecos.rc.arizona.edu From hinsen@dirac.cnrs-orleans.fr Mon Jun 29 11:51:37 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA24021 Mon, 29 Jun 1998 11:51:36 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.7/8.7) id RAA03864; Mon, 29 Jun 1998 17:51:24 +0200 (DFT) Date: Mon, 29 Jun 1998 17:51:24 +0200 (DFT) Message-Id: <199806291551.RAA03864@dirac.cnrs-orleans.fr> From: To: yliu@wesleyan.edu CC: chemistry@www.ccl.net In-reply-to: <199806280100.VAA17762@mail.wesleyan.edu> (message from Yongxing Liu on Sat, 27 Jun 1998 21:00:24 -0400 (EDT)) Subject: Re: CCL:Programs that can perform MD only in torsional space References: <199806280100.VAA17762@mail.wesleyan.edu> > I want to know if there exists one program that can perform Molecular > Dynamics Simulation only in torsional space. I also want to know related > algorithms and the degree of difficulty to implement such a program compared > with normal Cartesian MD programs. I know some programs can do this by You might be interested in these two papers: G.R. Kneller, K. Hinsen Generalized Euler equations for linked rigid bodies Phys. Rev. E 50, 1559 (1994) K. Hinsen, G.R. Kneller Influence of constraints on the dynamics of polypeptide chains Phys. Rev. E 52, 6868 (1995) The first paper derives the equations of motions for a system with arbitrary distance constraints using generalized coordinates (torsion angle dynamics is a special case). The second paper presents an implementation and application. The implementation is available as a set of Fortran subroutines that should be easy to integrate into any MD program (we used an old version of Gromos); write to me if you are interested. Please note that I didn't spend much effort to optimize the implementation. In my experience, constraint-type dynamics, in whatever way it is implemented, does not work well for significantly reduced coordinate sets, and is of little advantage for almost-complete coordinate sets, so I didn't want to invest any more effort. Another paper that could be of interest for you is L.M. Rice, A.T. Br"unger Torsion Angle Dynamics: Reduced Variable Conformational Sampling Enhances Crystallographic Structure Refinement Proteins 19, 277 (1994) It describes protein dynamics in phi-psi space (i.e. a subset of torsional angle space) for use in structure refinement, i.e. simulated annealing. For that application, the correctness of the dynamics is unimportant, so rather drastic constraints can be useful. But then you might be better off with some Monte-Carlo method if you don't care about dynamics. I suppose this method is implemented in some version of XPlor. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------