From chemistry-request@server.ccl.net Thu May 30 03:21:07 2002 Received: from ms1.uibk.ac.at ([138.232.1.201]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4U7L7C29040 for ; Thu, 30 May 2002 03:21:07 -0400 Received: from localhost (web-mail1.uibk.ac.at [138.232.1.225] Hannes.Loeffler@uibk.ac.at) by ms1.uibk.ac.at (8.11.3/E2) with ESMTP id g4U7L2k46538817 for ; Thu, 30 May 2002 09:21:05 +0200 (CEST) Received: from 62.47.210.85 ( [62.47.210.85]) as user c72409@mail1.uibk.ac.at by web-mail1.uibk.ac.at with HTTP; Thu, 30 May 2002 09:21:02 +0200 Message-ID: <1022743262.3cf5d2de65e32@web-mail1.uibk.ac.at> Date: Thu, 30 May 2002 09:21:02 +0200 From: Hannes Loeffler To: chemistry@CCL.net Subject: summary: diffusion coefficient from MSD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 62.47.210.85 Hello, I recently asked about details concerning the calculation of the diffusion coefficient from the mean square displacement. I wanted to know how long I should simulate to obtain meaningful results and why the MSD curve might be non-linear. In the following I will briefly summarize from the answers I received and my own investigations. General remarks: 1) If simulations are performed under PBCs the trajectory must be properly unfolded (revert PBCs) before any further calculation may be done. 2) Statistics is considerably improved if multiple time origins are taken into account. "Long" time: There seems to be some agreement that at least several hundred picoseconds are necessary to obtain meaningful results. The simulation time depends, of course, also on the ensemble size (single molecules naturally need longer simulation times). Non-linearity: 1) One cause may be insufficient statistics at long time. In that case a weighted linear fit may be helpful using the standard deviation as the weights. 2) Another problem may arise from translational and/or rotational movement of the total system. Error estimation: 1) The covariance matrix may be derived from the slope which yields a measure of the error bar. 2) Another method seems to be to plot ln(MSD) vs ln(t). The slope should be close to 1. 3) I found the paper from G. C. Lie and E. Clementi [Phys. Rev. A, 33(1986), 2679] very usful to interpret statical and dynamical properties in solution. These authors calculate the MSD for a water simulation separately for H's and O's. At short time (a few picoseconds) both MSDs develop into a straight line but different slope. However, since water must move as a single entity, the curves must have the same slope after some time. I want to thank everybody for help. I hope nobody minds if I do not copy all the response here to avoid wasting band width. People sending me valuable answers: Michael Brunsteiner, Kenneth Geisshirt, Richard Gillilan, Scott Feller, James Kubicki, David van der Spoel, Brian K. Peterson, Chas Simpson. Thanks again for all the help, Hannes. -- Hannes Loeffler | tel: +43-(0)512-507-5166 | fax: +43-(0)512-507-2714 http://www-c724.uibk.ac.at/staff/loeffler/ | mailto:Hannes.Loeffler@uibk.ac.at Institute for General, Inorganic and Theoretical Chemistry University of Innsbruck, Austria From chemistry-request@server.ccl.net Thu May 30 11:12:14 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4UFCEC06073 for ; Thu, 30 May 2002 11:12:14 -0400 Received: from igc.phys.chem.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g4UFCAx00486 for ; Thu, 30 May 2002 17:12:10 +0200 (MEST) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <3CF6414A.A7FA3597@igc.phys.chem.ethz.ch> Date: Thu, 30 May 2002 17:12:10 +0200 From: Stefan Portmann X-Mailer: Mozilla 4.76 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: WATOC'02: Last Call for Contributions! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Madam or Sir 6th WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS (WATOC'02) August 4-9, 2002, Palazzo dei Congressi, Lugano, Switzerland More than 100 talks and over 400 poster presentations in Theory, Computation and Information Science in Chemistry, Biochemistry and Materials Science. Don't miss this great event! Last Call for Contributions: Please submit an abstract for your contribution until the end of May using the online form at http://www.watoc02.ch (Deadline: May 31, 2002). WATOC'02 special issue of THEOCHEM: We are pleased to announce that Elsevier will publish a WATOC'02 special issue of THEOCHEM to appear in Spring 2003. You are therefore invited to submit a full paper. Information and Registration: http://www.watoc02.ch. Registrations are accepted until June 14, 2002. We are looking forward to see you in Lugano. Hans Peter Luethi and Stefan Portmann ETH Zurich From chemistry-request@server.ccl.net Thu May 30 10:07:56 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4UE7tC04835 for ; Thu, 30 May 2002 10:07:56 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 17DQao-0005pM-00 for chemistry@ccl.net; Thu, 30 May 2002 16:07:54 +0200 Message-ID: <3CF631E1.8090103@mpi-bpc.mpg.de> Date: Thu, 30 May 2002 16:06:25 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: questions Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit I am trying to calculate the electron density and electrostatic potential for some pteridine analogues. I have several questions about that. I am using as model the desciption of this type of calculation for azulene and nafthalene described on www.gaussian.com. I also must say that I am a beginner with Gaussian. 1. If I am using RBecke3LYP method for calculating the density and ep is it necessary that the optimization run prior to these calculations is done using the same method or can I simply use a structure that was optimized using HF. 2. By your experience which DFMethod gives the best results for the electron density and ep? 3. I found this explaination on the site ("The theoretical model used in this study was the RBecke3LYP method with a 6-31G(D) basis set. The optimized geometry was determined by minimizing the energy with respect to the nuclear coordinates. This was followed by a calculation of the frequencies of vibration to verify that the structure was a minimum and to compute the thermal energy at 300 Kelvin"). Can somebody explain how can one verify from the freq. of vibration if the structure was a minimum? 4. Did somebody ever calculated these properties for 2-amino purine in order to compare them to that of Adenine. If yes could you please supply me a reference so that I can look up. Thanks in advance for any kind of suggestions, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Thu May 30 14:32:07 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4UIW5C10780 for ; Thu, 30 May 2002 14:32:06 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 17DUiS-0002JA-00 for chemistry@ccl.net; Thu, 30 May 2002 20:32:04 +0200 Message-ID: <3CF66FCF.5030506@mpi-bpc.mpg.de> Date: Thu, 30 May 2002 20:30:39 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: Cube in gaussian Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Can somebody give me in a few words some criterias of chosing the paramter that specifies the number of points to use for Cube. For instance what would be more accurate Cube(40,Density) or Cube(100,Density)? Thanks, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Thu May 30 12:02:09 2002 Received: from orionl0.ccf.auth.gr ([155.207.2.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4UG28C07251 for ; Thu, 30 May 2002 12:02:08 -0400 Received: from chem011 (chem011.chem.auth.gr [155.207.64.94]) by orionl0.ccf.auth.gr (8.12.3/8.12.3/8.12.3) with SMTP id g4UG26X4018407 for ; Thu, 30 May 2002 19:02:06 +0300 (EET DST) Organization: Message-ID: <002201c207f3$3deced60$5e40cf9b@chem.auth.gr> From: "temper" To: Subject: RWF_problem Date: Thu, 30 May 2002 19:01:21 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001F_01C2080C.62F9C100" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Virus-Scanned: by mail.auth.gr, virus data file v4204 created May 22 2002 This is a multi-part message in MIME format. ------=_NextPart_000_001F_01C2080C.62F9C100 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable I split the RWF into 8 segments=20 %rwf=3D1,250mw,2,250mw,3,250mw,4,250mw,5,250mw,6,250mw,7,250mw,8,250mw %m=3D450mb #p mp2/6-311++(2d,p) MaxDisk=3D2000mw nmr but i see a termination error window. The error from the output is shown below: WUsed=3D 86707699 WInt=3D 1018368 WEnd=3D 1138054656 Dk804=3D 411771500. Dk1111=3D 0. Dk1112=3D 1282374100. MaxDsk=3D 2097152000 LAFull=3D 94119200 DskLim=3D 2097152000. NUsed=3D 407288691. 3765885195. 2571205219. 2603493867. 2119164147. = 1796277667. In DefCFB: NBatch=3D 1, ICI=3D 28, ICA=3D245, LFMax=3D 9 Large arrays: LIAPS=3D 0, LIARS=3D -2034761936 = words. No file to extend for IUnit=3D 1 -- out of disk space. Error termination in NtrErr: NtrErr called from NtrExt. When i split the RWF into 9 segments i have the same error. Maybe i can split the RWF into a maximum of 8 segments. The operating system is WINDOWS2000. The program is GAUSSIAN (G98wA.11). What can i do? Thanks in advance. ------=_NextPart_000_001F_01C2080C.62F9C100 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
I split the = RWF into 8=20 segments
%rwf=3D1,250mw,2,250mw,3,250mw,4,250mw,5,250mw,6,250mw,7,250mw,8= ,250mw
%m=3D450mb
#p=20 mp2/6-311++(2d,p)  MaxDisk=3D2000mw  nmr
but i see a = termination error=20 window.
The error from the output is = shown=20 below:
WUsed=3D    =20 86707699  WInt=3D       1018368  = WEnd=3D    1138054656
 Dk804=3D    = 411771500.=20 Dk1111=3D           0. = Dk1112=3D  1282374100.
 MaxDsk=3D  2097152000 =20 LAFull=3D    94119200  DskLim=3D =20 2097152000.
 NUsed=3D  407288691. 3765885195. 2571205219. = 2603493867.=20 2119164147. 1796277667.
 In DefCFB: NBatch=3D  1, ICI=3D = 28, ICA=3D245,=20 LFMax=3D =20 9
           &n= bsp;=20 Large arrays: = LIAPS=3D          =20 0, LIARS=3D -2034761936 words.
 No file to extend for = IUnit=3D  1 --=20 out of disk space.
 Error termination in NtrErr:
 NtrErr = called=20 > from NtrExt.
When i split the RWF into 9 = segments i=20 have the same error.
Maybe i can split the RWF = into a maximum=20 of 8 segments.
The operating system is=20 WINDOWS2000.
The program is GAUSSIAN=20 (G98wA.11).
What can i do?
Thanks in=20 advance.
------=_NextPart_000_001F_01C2080C.62F9C100-- From chemistry-request@server.ccl.net Thu May 30 16:20:34 2002 Received: from hisar.cc.boun.edu.tr ([193.140.192.229]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4UKKWC12407 for ; Thu, 30 May 2002 16:20:33 -0400 Received: by hisar.cc.boun.edu.tr (Postfix, from userid 4210) id CA08F135E; Thu, 30 May 2002 23:18:35 +0300 (EET DST) Received: from localhost (localhost [127.0.0.1]) by hisar.cc.boun.edu.tr (Postfix) with ESMTP id BCC84FCB; Thu, 30 May 2002 23:18:35 +0300 (EET DST) Date: Thu, 30 May 2002 23:18:35 +0300 (EET DST) From: "Alimet S. Ozen" X-Sender: ozensem@hisar.cc.boun.edu.tr To: Vlad Cojocaru Cc: CCL list Subject: Re: CCL:questions In-Reply-To: <3CF631E1.8090103@mpi-bpc.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I might have an answer for that question: On Thu, 30 May 2002, Vlad Cojocaru wrote: > 3. I found this explaination on the site ("The theoretical model used in > this study was the RBecke3LYP method with a 6-31G(D) basis set. The > optimized geometry was determined by minimizing the energy with respect > to the nuclear coordinates. This was followed by a calculation of the > frequencies of vibration to verify that the structure was a minimum and > to compute the thermal energy at 300 Kelvin"). Can somebody explain how > can one verify from the freq. of vibration if the structure was a minimum> > I couldn't find the explanation you mentioned but as far as I know, a stationary point(a local or a global minumum or a transition state) on a potential energy surface is where the net force is zero, meaning the first derivative of energy wrt nuclear coordinates (or the gradient) is zero.In addition to that, at minimum, the second derivative of energy must be greater than 0 or in other words all the eigenvalues of the hessian matrix must be positive.(If one eigenvalue is negative then this is a transition state) Second derivatives of energy are related to the harmonic force constants that are further related to the vibrational frequencies.So, if you have all-positive frequencies than this verifies that the structure is a minimum..but cannot tell if it is a global or a local one.. If you have one negative or 'imaginary' frequency than this is a transition state..maximum in one dimension but minimum in all the others.. you can refer Alan Hinchliffe's book 'modelling molecular structures' (or Frank Jensen's 'introduction to computational chemistry') for a better discussion.. Best regards Alimet "Real value: is not the one whose presence fills an empty space but the one whose absence creats one" Ozdemir Asaf ozensem@boun.edu.tr alimetsema@yahoo.com http://www.geocities.com/alchemistrial