From chemistry-request@server.ccl.net Fri Mar 7 04:46:30 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h279kTa28249 for ; Fri, 7 Mar 2003 04:46:29 -0500 Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.12.8/jtpda-5.4) with ESMTP id h279kSCc095853 for ; Fri, 7 Mar 2003 10:46:28 +0100 (CET) Received: from ccr.jussieu.fr (verdi.div.jussieu.fr [134.157.75.160]) by moka.ccr.jussieu.fr (8.10.0/jtpda-5.3.3) with ESMTP id h279kSa2003002 for ; Fri, 7 Mar 2003 10:46:28 +0100 Sender: seb@ccr.jussieu.fr Message-ID: <3E68E8A1.79F32387@ccr.jussieu.fr> Date: Fri, 07 Mar 2003 10:44:49 -0800 From: Sebatien Laugaro Organization: Pharmacochime Moleculaire X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: interactions acetate-Ca2+ Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Antivirus: scanned by sophie at shiva.jussieu.fr I 'm a student who begins to work on molecular modelling. I try to calculate interactions between acetate and calcium ion. I use gaussian98 with a minimal basis set STO-3G for calculation. Here, you 'll find the input files that I 've used I've obtained, for the energy, the following values : acetate HF= -224.048329 a.u. acetate-Ca2+ HF= -894.1014679 a.u. It seems that values are very important for the simple molecule. Can I have your opinion on this results. Thanks # HF/STO-3G opt Test acetate -- No Title Specified -- -1 1 C H,1,R2 H,1,R3,2,A3 H,1,R4,2,A4,3,D4,0 C,1,R5,2,A5,3,D5,0 O,5,R6,1,A6,2,D6,0 O,5,R7,1,A7,6,D7,0 Variables: R2=1.09000004 R3=1.09000022 R4=1.08999992 R5=1.53892936 R6=1.35999971 R7=1.36000012 A3=109.442489 A4=109.44245828 A5=109.49999294 A6=119.99998274 A7=120.00001344 D4=-119.92951754 D5=120.03523743 D6=-161.48330442 D7=180. # HF/STO-3G opt Test acetate-Ca2+ -- No Title Specified -- 1 1 C H,1,R2 H,1,R3,2,A3 H,1,R4,2,A4,3,D4,0 C,1,R5,2,A5,3,D5,0 O,5,R6,1,A6,2,D6,0 O,5,R7,1,A7,6,D7,0 Ca,5,R8,1,A8,6,D8,0 Variables: R2=1.09000004 R3=1.09000022 R4=1.08999992 R5=1.53892936 R6=1.35999971 R7=1.36000012 R8=1.93149253 A3=109.442489 A4=109.44245828 A5=109.49999294 A6=119.99998274 A7=120.00001344 A8=166.15685408 D4=-119.92951754 D5=120.03523743 D6=-161.48330442 D7=180. D8=-100.01757363 my e-mail is ; laugaro@ccr.jussieu.fr From chemistry-request@server.ccl.net Fri Mar 7 07:10:58 2003 Received: from spearnet.net ([65.170.133.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h27CAwa01153 for ; Fri, 7 Mar 2003 07:10:58 -0500 Received: from cornell.edu [67.193.134.27] by spearnet.net with ESMTP (SMTPD32-6.06) id A10E11D70112; Fri, 07 Mar 2003 06:31:10 -0600 Date: Fri, 7 Mar 2003 07:14:04 -0500 Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostati Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v551) Cc: Charles Xie , CHEMISTRY@ccl.net To: Konrad Hinsen From: Richard Gillilan In-Reply-To: <200303062021.11954.hinsen@cnrs-orleans.fr> Message-Id: <4A0E5C1B-5096-11D7-81D8-003065963E2C@cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.551) > > I wonder if standard MD is the best choice for that kind of system. > Some > adaptive step-size integrator that slows down only in case of > near-collisions > might be better. Or perhaps even a scheme similar to those used for > hard-sphere systems, where the time step is obtained by estimating the > time > until the next collision. > -- > High-energy collisions would certainly require a smaller time step at the moment of the collision, but at this time the van der Waal's repulsion term should far outweigh any electrostatics at this close range since it climbs as (1/r)^14. I have often thought an adaptive, but symplectic integration scheme would be very useful. This kind of thing also happens when I do rigid body mechanics on whole proteins in solution. When proteins are far away you can take large time steps. I believe this is the basic idea behind the RESPA method developed by B. Berne and coworkers. (see JCP 97 (3) pp1990-2001 (1992)) Richard From chemistry-request@server.ccl.net Fri Mar 7 08:41:04 2003 Received: from imaph.bas-net.by ([80.94.164.102]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h27Df0a03967 for ; Fri, 7 Mar 2003 08:41:00 -0500 Received: from igor (igor [10.1.1.15]) by imaph.bas-net.by (8.12.5/8.12.5) with ESMTP id h27EB3hF014305 for ; Fri, 7 Mar 2003 16:11:03 +0200 Date: Fri, 7 Mar 2003 15:41:37 +0200 From: Igor Avilov X-Mailer: The Bat! (v1.45) Educational Reply-To: Igor Avilov X-Priority: 3 (Normal) Message-ID: <119606382702.20030307154137@imaph.bas-net.by> To: chemistry@ccl.net Subject: point charges in Gaussian98 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL experts! Could you help me with thw following problem, please? I need to calculate the excited states of a molecule (by TDDFT with the use of Gaussian98) having high symmetry using the geometry optimized beforehand. I want to place point charges in such a way that the overall symmetry is conserved. But when I indicate the coordinates of the point charges in cartesian coordinates I break the symmetry somehow. Is there a way to incorporate the point charges into Z-matrix? Best regards, Igor Avilov. From chemistry-request@server.ccl.net Fri Mar 7 03:01:12 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h27815a11443 for ; Fri, 7 Mar 2003 03:01:07 -0500 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id PAA19188 for ; Fri, 7 Mar 2003 15:46:35 +0800 Message-Id: <200303070746.PAA19188@mx1.ustc.edu.cn> Date: Fri, 7 Mar 2003 15:48:52 +0800 From: 丁迅雷 Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: In g98, what Basis suit for the calculation with Au? Organization: 中国科大选键化学实验室 X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon730386733845_=====" This is a multi-part message in MIME format. --=====000_Dragon730386733845_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xzo7oNCg0KoaGhoUluIGc5OCwgd2hhdCBCYXNpcyBzdWl0IGZvciB0aGUgY2FsY3Vs YXRpb24gd2l0aCBBdSA/DQoJDQpUaGFuayB5b3UgZm9yIHlvdXIgaGVscCGhoaGhoaGhoaGhoaGh oaGhDQogCQkJCQ0KoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoURpbmcgWHVubGVpDQqhoaGh oaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhMjAwMy0wMy0wNw0KX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fXw0KRGluZyBYdW5sZWksIFBoLkQuIENhbmRpZGF0ZQ0K T3BlbiBMYWJvcmF0b3J5IG9mIEJvbmQgU2VsZWN0aXZlIENoZW1pc3RyeQ0KVW5pdmVyc2l0eSBv ZiBTY2llbmNlICYgVGVjaG5vbG9neSBvZiBDaGluYQ0KSGVmZWksIEFuaHVpIDIzMDAyNiwgUC5S LkNoaW5hDQpUZWwuOiAwMDg2LTU1MS0zNjAzNDE4DQpGYXguOiAwMDg2LTU1MS0zNjAyOTY5DQpF LW1haWw6IGR4bEBtYWlsLnVzdGMuZWR1LmNuDQpIdHRwOi8vd3d3LmJzYy51c3RjLmVkdS5jbi9+ ZHhsDQo= --=====000_Dragon730386733845_===== Content-Type: image/gif; name="LittleBoy.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy.GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon730386733845_=====-- From chemistry-request@server.ccl.net Fri Mar 7 03:01:12 2003 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2781Ba11445 for ; Fri, 7 Mar 2003 03:01:11 -0500 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Fri, 7 Mar 2003 09:00:31 +0100 Message-ID: <004001c2e47f$ede591e0$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Dr. Andreas Klamt" , References: <3E676049.6020407@cosmologic.de> Subject: Re: CCL:Full description of SDF file format Date: Fri, 7 Mar 2003 09:02:42 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-15" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 MDL's file formats are available from: http://www.mdli.com/downloads/ctfile/ctfile_subs.html Tamas -------------------------- Prof. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ------------------- ----- Original Message ----- From: "Dr. Andreas Klamt" To: Sent: Thursday, March 06, 2003 15:50 Subject: CCL:Full description of SDF file format > Does anyone have a full description of the sdf-file format available? > > Thanks in advance > > Andreas > -- > -------------------------------------------------------------------------------- > Dr. Andreas Klamt > COSMOlogic GmbH&CoKG > Burscheider Str. 515 > 51381 Leverkusen, Germany > > Tel.: +49-2171-73168-1 > Fax: +49-2171-73168-9 > e-mail: klamt@cosmologic.de > web: www.cosmologic.de > -------------------------------------------------------------------------------- > COSMOlogic > Your Competent Partner for > Computational Chemistry and Fluid Thermodynamics > -------------------------------------------------------------------------------- > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Mar 6 17:16:37 2003 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26MGYa29187 for ; Thu, 6 Mar 2003 17:16:35 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.8/8.12.8) with ESMTP id h26MGWFj021066; Thu, 6 Mar 2003 17:16:32 -0500 (EST) Date: Thu, 6 Mar 2003 17:00:38 -0500 From: Rick Venable To: Charles Xie cc: CHEMISTRY@ccl.net, bob@concord.org Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostatic forces In-Reply-To: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Message-ID: References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I feel obliged to comment that CHARMM most certainly *does* conserve energy with NVE, and that is put the test frequently as new methods are developed and added. Normally, a 1 fs timestep is fine, and one can even use a 2 fs timestep if bonds to hydrogen are constrained via SHAKE. Most of the testing and usage is done with condensed phase systems, mostly fluid. I should note that systems with a small number of particles (e.g. less than a few hundred water molecules) behave poorly and may appear not to conserve energy because of large fluctuations in energy and forces. There was a minor bug that led to non-conservation of energy for extended system dynamics (NPT, NVT, etc.) in the initial CHARMM implementation, but that has been fixed. I am currently running some NPT simulations with 2 fs timestep and SHAKE which conserve the total system Hamiltonian quite nicely. The system includes numerous zwitterions with full formal +1 and -1 charges (phosphocholine lipids). Allen & Tildesley discuss energy conservation in section 3.5, "Checks on Accuracy"; it's the first topic mentioned. On Thu, 6 Mar 2003, Charles Xie wrote: > I have a general question about totoal energy conservation of classical > molecular dynamics (MD) in the presence of electrostatic forces. > > Total energy is perfectly conserved when we do a typical MD with > only the wan der Waals (Lennard-Jones) potentials, using a time > step of one femtosecond (e.g. for the Argon gas as a classical example). > > Problems, however, arise when molecules are charged. Because > electrostatic forces are much more long-ranged (1/r dependence) and > typically stronger, the magnitude of electrostatic forces on atoms can > be several hundred (or even thousand) times greater than that of van > der Waals forces. As a result, the time step has to be accordingly > reduced for two or three orders of magnitude, in order for the total > energy to conserve. This means a time step of 0.001-0.01 femtosecond > has to be applied. > > (EXPLAIN: Most standard algorithms, such as the Verlet method, the Gear > predictor-corrector method and the Runge-Cutta method, depend on using > the term a*dt^2 to compute the solution stepwisely, where a is the > acceleration, > dt is the time step. If this term is too large, the numerical error will > rapidly > propogate, and the solution will diverge. Compared with pure Lennard-Jones > simulations, adding the electrostatic forces increase accelerations. > Therefore, > dt must be decreased in order to keep a*dt^2 down.) > > I can see only two ways to solve this problem, both of which turn out to be > impractical, as you will see later. > > One is to accept the reality, use a smaller time step. But, reducing the time > step to 0.001 femtosecond will slow down the simulation 1000 times (in > comparison to pure Lennard-Jones simulations). You will probably never see > any emerging behavior of the model because losing your temper. > > The other way around is to use smaller charges, as most molecular mechanics > force fields do. For example, instead of using 1 for a free radical's charge, > one can use 0.01 (and self-explain that this is an effective-field > approximation). > While this would maintain energy conservation, you might not see the > emerging behaviors due to charges either --- because the electrostatic forces > are so weaker than they ought to be, they might not be able to produce > results that only strong interactions can exhibit, such as self-organization. > > Energy conservation is generally not an concern for most classic molecular > dynamics simulations that assume a heat bath (for controlling the temperature > to a desired value, thus remove the numerical errors resulted from large > a*dt^2). > However, getting the energetics right is of paramount importance to modeling > exoergicity/endoergicity of chemical reactions. Unfortunately, I am not aware > of anyone mentioning this before. All the molecular simulation books I have > (Allen and Tildesley, Leach, Rapaport and so on) do not even mention it at all. > My prior experience with CHARMm v27, if I was doing it right, is that it > doesn't > seem to do energy conservation, even though the NVE protocol is literally > specified. > > I would greatly appreciate any advice and opinion. > > Thank you, > > Charles Xie > > International Center > The Concord Consortium > www.concord.org > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= "Don't blame me, I voted for Kang." Homer ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=