From chemistry-request@server.ccl.net Fri May 16 03:08:51 2003 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4G78oJ21120 for ; Fri, 16 May 2003 03:08:51 -0400 Received: from ac12 by wn1.sci.kun.nl via ac12.sci.kun.nl [131.174.179.19] with ESMTP id h4G78os8003161 (8.12.9/3.58); Fri, 16 May 2003 09:08:50 +0200 (MEST) Content-Type: text/plain; charset="iso-8859-1" From: "E.L. Willighagen" Reply-To: egonw@sci.kun.nl To: Rick Venable , chemistry@ccl.net Subject: Re: CCL:molecular animation tools Date: Fri, 16 May 2003 09:08:49 +0200 User-Agent: KMail/1.4.2 References: <200305151012.16286.weiz@mail.rochester.edu> In-Reply-To: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200305160908.49838.egonw@sci.kun.nl> On Thursday 15 May 2003 23:47, Rick Venable wrote: > My questions are: > > Are there other inexpensive or free media players for M$ and Mac that > can handle MPEG1 and can provide a way to set the playback speed? > > Can anyone recommend other inexpensive animation software for making > "movies" in a common format from a series of still frames? > > Is anyone aware of conversion tools, that might convert MPEG1 to > QuickTime or other common format? Dear R. Venable, as project leader of the Jmol project I am much interested in receiving a copy of the summary on this topic. Jmol (jmol.sf.net) itself is used for displaying animations and can export movies by means of PovRay... The summary may help the project extend Jmol to be able to export full movies in a future version. Looking forward to hearing about the answers you get on the above questions, kind regards, Egon Willighagen http://jmol.sourceforge.net/ PS. Jmol is OpenSource and written in Java. From chemistry-request@server.ccl.net Fri May 16 04:43:38 2003 Received: from artemis.rus.uni-stuttgart.de ([129.69.1.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4G8hbJ08863 for ; Fri, 16 May 2003 04:43:38 -0400 Received: from itbntw22 (itbntw22.biologie.uni-stuttgart.de [129.69.145.79]) by artemis.rus.uni-stuttgart.de with ESMTP id KAA19822 for ; Fri, 16 May 2003 10:43:37 +0200 (MET DST) env-from (fabian.boes@po.uni-stuttgart.de) Message-ID: <200305161043290653.B27DF3D1@po.uni-stuttgart.de> X-Mailer: Calypso Version 3.30.00.00 (1) Date: Fri, 16 May 2003 10:43:29 +0100 From: "Fabian Boes" To: chemistry@ccl.net Subject: Re:molecular animation tools Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4G8hcJ08868 hello ... >Can anyone recommend other inexpensive animation software for making >"movies" in a common format from a series of still frames? i am using the following windows based software for doing my animations: "Pymol" -> for creating the animation and saving single .png files for each frame "IrfanView" -> for converting the .png into .bmp files "pjBmp2Avi" -> for creating an uncompressed .avi file out of the bitmap (or .tga ) files. frame rate can be specified as well as the keyframes. the resulting animation in uncompressed .avi format is very large (approx. 900 MB for 40 sec. with 640x480 resolution, 25fps). thus i compress it using the programm "Virtualdub" with the open-source video codec "Xvid", which is similar to the popular "DivX" codec. "Virtualdub" is not able to save .mpeg files, but you can use "TMPGEnc" to create .mpeg files out of your uncompressed .avi file. all of the programs i mentioned are - as far as i now - open-source, freeware or shareware, excluding "TMPGEnc" which is free only for personal use (see their website for more details). here are the links: "Pymol" -> http://www.pymol.org "IrfanView" -> http://www.irfanview.com "pjBmp2Avi" -> http://www.cspltd.ndirect.co.uk/graphics/anim.htm "Virtualdub" -> http://www.virtualdub.org/ "XVid" -> http://www.xvid.org (just the source-code, a comiled version can be found here: http://www.roeder.goe.net/%7Ekoepi/xvid.shtml) "TMPGEnc" -> http://www.tmpgenc.net/ hope i could help you a little bit, if there are any questions left, feel free to ask. fabian --------------------------------------------------------------- Fabian Bös Institute of Technical Biochemistry University of Stuttgart / Germany Phone: +49-711-6857481 Fax: +49-711-6853196 Email: fabian.boes@po.uni-stuttgart.de http://www.itb.uni-stuttgart.de -------------------------------------------------------------- From chemistry-request@server.ccl.net Thu May 15 15:06:02 2003 Received: from Lilly.com ([40.33.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4FJ61J21242 for ; Thu, 15 May 2003 15:06:01 -0400 Received: from LILLY.COM ([40.59.1.39]) by INET.D48.LILLY.COM (PMDF V6.1-1 #30673) with ESMTP id <01KVX8VR421E006547@INET.D48.LILLY.COM> for CHEMISTRY@ccl.net; Thu, 15 May 2003 14:06:00 -0500 (EST) Received: from mcntusmail25.d51.lilly.com (mcntusmail25.d51.lilly.com [40.1.134.25]) by NEWMAN.D52.LILLY.COM (PMDF V6.1-1 #30673) with ESMTP id <01KVX8VQJ638000P40@NEWMAN.D52.LILLY.COM> for CHEMISTRY@ccl.net; Thu, 15 May 2003 14:05:59 -0500 (EST) Content-return: prohibited Date: Thu, 15 May 2003 14:05:58 -0500 From: WU_GUOSHENG@Lilly.com Subject: Re: CCL:Error estimation of gibbs free energy To: CHEMISTRY@ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.07a May 14, 2001 Content-type: multipart/alternative; boundary="=_alternative 0068EB6A05256D27_=" X-MIMETrack: Serialize by Router on USMAIL25/AM/LLY(Release 5.0.10 |March 22, 2002) at 05/15/2003 02:05:59 PM, Serialize complete at 05/15/2003 02:05:59 PM This is a multipart message in MIME format. --=_alternative 0068EB6A05256D27_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thanks to Ioana for the link on error propogation. http://mulliken.chem.hope.edu/~polik/Chem345-2000/errorpropagation.htm which tells the difference between systematic error & random error.=20 However, it seems not easy to know which is which at times. Especially for = the case of free energy?=20 So maybe it's reasonable to include all of the terms as I did in my last=20 email, then see which one we can forget in practical applications. Guosheng Wu, Ph.D. Eli Lilly & Company Ioana Cozmuta 05/15/2003 01:35 PM =20 To: WU=5FGUOSHENG@Lilly.com cc: CHEMISTRY@ccl.net Subject: Re: CCL:Error estimation of gibbs free energy Hi Guosheng, > From the top of my head, that formula comes from a Taylor expansion in which you neglect the higher-order terms. Honestly, the best info I have on error propagation are my hand written notes from the courses I followed during undergrad/grad studies. However, if you do a search on google with the following terms: general formula error propagation it gives lots of references. The most frequently mentioned reference I see is Taylor, J. R., "An introduction to Error Analysis", University Science Books, 1982. I also think that any book on numerical analysis should have at least a chapter that covers error propagation. See also: http://mulliken.chem.hope.edu/~polik/Chem345-2000/errorpropagation.htm Regards, Ioana **************************************************************************** * Ioana Cozmuta, PhD * * * NASA-AMES Research Center * "Gravitation can not be held=20 responsible* * Mail Stop 230-3 * for people falling in love" * * Moffet Field,CA 94035 * * * phone: (650) 604-0993 * Albert=20 Einstein* * fax: (650) 604-0350 * (1879-1955)=20 * **************************************************************************** On Thu, 15 May 2003 WU=5FGUOSHENG@Lilly.com wrote: > Dear Ioana, > > Could you please point out if there is any reference for your equation? > > I am sure there must be such kind of thing in some data analysis books, > but it's just inconvenient for me to find it at this moment. > > It seems to me the straightforwad way to get an error estimation is > by the basis calculus, like following (with similar presentation to > yours): > > for f =3D f(x1, x2, ...), > > (del=5Ff)=3D (df/dx1)*(del=5Fx1) + (df/dx2)*(del=5Fx2) + ... > > Then, (del=5Ff)^2 can be the next form, if one has the interest: > > (del=5Ff)^2=3D (df/dx1)^2 * (del=5Fx1)^2 + (df/dx2)^2 * (del=5Fx2)^2 > + 2*(df/dx1)* (del=5Fx1) * (df/dx2) * (del=5Fx2) + ... > > So for your example if f=3D x+y then (del=5Ff) =3D (del=5Fx)+(del=5Fy) > > if f =3D x*y then simply > del=5Ff =3D x * (del=5Fy) + y * (del=5Fx) > > If one like, (del=5Ff)/f =3D (del=5Fx)/x + (del=5Fy)/y > > or [(del=5Ff)/f]^2 =3D (del=5Fx/x)^2 + (del=5Fy/y)^2 > + 2 * (del=5Fx)*(del=5Fy)/(x*y) > > Of course, for practical usage, one may overlook one or more terms if=20 they > are much smaller than others. > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Thanks for your attention. > > Sincerely, > > Guosheng > > Guosheng Wu, Ph.D. > Eli Lilly & Company > > > > > > Ioana Cozmuta > Sent by: Computational Chemistry List > 05/14/2003 01:32 PM > > > To: "'CHEMISTRY@ccl.net'" > cc: > Subject: CCL:Error estimation of gibbs free energy > > > Hi, > > The most general formula from which you can always estimate the error > del=5Ff of a function f(x1, x2, x3, ...xn) is > > (del=5Ff)^2=3D (df/dx1)^2*del=5Fx1^2+(df/dx2)^2*del=5Fx2^2+... > > where df/dxi are partial derivatives of the function f with respect to=20 xi > (i=3D1,n) and del=5Fxi are the individual errors. > > So for example if f=3D x+y then (del=5Ff)^2 =3D (del=5Fx1)^2+(del=5Fx2)^2 > if f =3D x*y then (delf/f)^2=3D (del=5Fx/x)^2+(del=5Fy/y)^2 > > If x1, ...xn are functions of other variables I find the general formula > above (with derivatives) much easier to use. > > Ioana > > On Wed, 14 May 2003, VITORGE Pierre 094605 wrote: > > > d(dG) =3D square root([d(dH)]^2 + [d(dS)]^2) > > cannot be true, if dh=3D0 and T is constant the above Eq. gives > > d(dG) =3D d(dS) > > while it is of course > > d(dG) =3D T d(dS) > > > > You probably mean: > > d(DG) =3D square root([d(DH)]^2 + [(Td(DS)+(DS)dT)]^2)? > > or > > d(DG) =3D square root([d(DH)]^2 + [Td(DS)]^2 + [(DS)dT]^2)? > > > > Pierre Vitorge > > CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-CNRS-Universite d'Evry) > > Universite d'Evry UMR 8587 > > pierre.vitorge@cea.fr > > http://perso.club-internet.fr/vitorgen/pierre/pierre.html > > > > > > -----Message d'origine----- > > De: Dr. Richard L. Wood [mailto:rlw28@cornell.edu] > > Date: lundi 12 mai 2003 15:58 > > =C0: Wong Lai Ho > > Cc: CHEMISTRY@ccl.net > > Objet: CCL:Error estimation of gibbs free energy > > > > > > Wouldn't the following be true > > > > d(dG) =3D square root([d(dH)]^2 + [d(dS)]^2)? > > > > dG is delta G, d(dG) is the error in delta G, dH is delta H, d(dH) is > the > > error > > in delta H, dS is delta S and d(dS) is the error in delta S. > > > > This is taken from a simple error propagation analysis as taught in=20 some > > physical/analytical chemistry laboratories. > > > > Richard > > > > Wong Lai Ho wrote: > > > > > Dear CCLers, > > > > > > I have a question regarding error estimation of the experimental > values of > > > gibbs free energy. > > > As we knows that: > > > delta G(formation) > > > =3D delta H(formation) > > > - Temp * [entropy(molecule)-sum(entropy(atoms to form the > molecules))] > > > > > > Can I claim that the experimental error bar of the gibbs free > energy(delta > > > G) is equal to the error bar of the enthalpy change of=20 formation(delta > H)? > > > (since the error introduced by the entropy is usually very small) > > > Is there any papers or books talking about this error? > > > > > > I would be grateful if you can give some comments on this claim. > > > > > > Larry > > > > > > > -- > > Richard L. Wood, Ph. D. > > Physical/Computational Chemist > > Post-doctoral Associate > > Department of Chemistry > > Trinity University, San Antonio, TX 78212 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -=3D This is automatically added to each message by mailing script =3D- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@osc.= edu > > > > > > > > --=_alternative 0068EB6A05256D27_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Thanks to Ioana for the link on erro= r propogation.

http://mulliken.chem.hope.edu/~poli= k/Chem345-2000/errorpropagation.htm

which tells the difference between s= ystematic error & random error.

However, it seems not easy to know w= hich is which at times. Especially for the case of free energy?
So maybe it's reasonable to include = all of the terms as I did in my last email, then see which one we can forge= t in practical applications.

Guosheng Wu, Ph.D.
Eli Lilly & Company




Ioana Cozmuta <ioana@nas.nasa.= gov>

05/15/2003 01:35 PM

       
        To: &nbs= p;      WU=5FGUOSHENG@Lilly.com
        cc: &nbs= p;      CHEMISTRY@ccl.net
        Subject:=        Re: CCL:Error estimation of gibbs free energy



Hi Guosheng,

> From the top of my head, that formula comes from a Taylor expansion in
which you neglect the higher-order terms.

Honestly, the best info I have on error propagation are my hand written
notes from the courses I followed during undergrad/grad studies.
However, if you do a search on google with the following terms:
general formula error propagation
it gives lots of references.
The most frequently mentioned reference I see is
Taylor, J. R., "An introduction to Error Analysis", University Sc= ience
Books, 1982.
I also think that any book on numerical analysis should have at least a
chapter that covers error propagation.
See also:
http://mulliken.chem.hope.edu/~polik/Chem345-2000/errorpropagation.htm

Regards,
Ioana

***************************************************************************= *
* Ioana Cozmuta, PhD            *   &nbs= p;                     &n= bsp;                     =                      = ;                    *
* NASA-AMES Research Center     *  "Gravitation can not= be held responsible*
* Mail Stop 230-3               *  = for people falling in love"             =                      = ;   *
* Moffet Field,CA 94035         *       =                      = ;                     &nb= sp;                     &= nbsp;                  *
* phone: (650) 604-0993         *       =                     Alber= t Einstein*
* fax:   (650) 604-0350         *     &n= bsp;                     =   (1879-1955)  *
***************************************************************************= *

On Thu, 15 May 2003 WU=5FGUOSHENG@Lilly.com wrote:

> Dear Ioana,
>
> Could you please point out if there is any reference for your equation= ?
>
> I am sure there must be such kind of thing in some data analysis books= ,
> but it's just inconvenient for me to find it at this moment.
>
> It seems to me the straightforwad way to get an error estimation is
> by the basis calculus, like following (with similar presentation to
> yours):
>
> for  f =3D f(x1, x2, ...),
>
> (del=5Ff)=3D (df/dx1)*(del=5Fx1) + (df/dx2)*(del=5Fx2) + ...
>
> Then, (del=5Ff)^2 can be the next form, if one has the interest:
>
> (del=5Ff)^2=3D (df/dx1)^2 * (del=5Fx1)^2 + (df/dx2)^2 * (del=5Fx2)^2 >          + 2*(df/dx1)* (del=5Fx1) * (df/dx2) = * (del=5Fx2) + ...
>
> So for your example if f=3D x+y then (del=5Ff) =3D (del=5Fx)+(del=5Fy)=
>
> if f =3D x*y then simply
>                 del=5Ff =3D x = * (del=5Fy) + y * (del=5Fx)
>
> If one like, (del=5Ff)/f =3D (del=5Fx)/x + (del=5Fy)/y
>
>     or   [(del=5Ff)/f]^2 =3D (del=5Fx/x)^2 + (del=5Fy/y= )^2
>                     =    + 2 * (del=5Fx)*(del=5Fy)/(x*y)
>
> Of course, for practical usage, one may overlook one or more terms if = they
> are much smaller than others.
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Thanks for your attention.
>
> Sincerely,
>
> Guosheng
>
> Guosheng Wu, Ph.D.
> Eli Lilly & Company
>
>
>
>
>
> Ioana Cozmuta <ioana@nas.nasa.gov>
> Sent by: Computational Chemistry List <chemistry-request@ccl.net>= ;
> 05/14/2003 01:32 PM
>
>
>         To:     "'CHEMISTRY@ccl.net= '" <CHEMISTRY@ccl.net>
>         cc:
>         Subject:        CCL:Er= ror estimation of gibbs free energy
>
>
> Hi,
>
> The most general formula from which you can always estimate the error<= br> > del=5Ff of a function f(x1, x2, x3, ...xn) is
>
> (del=5Ff)^2=3D (df/dx1)^2*del=5Fx1^2+(df/dx2)^2*del=5Fx2^2+...
>
> where df/dxi are partial derivatives of the function f with respect to= xi
> (i=3D1,n) and del=5Fxi are the individual errors.
>
> So for example if f=3D x+y then (del=5Ff)^2 =3D (del=5Fx1)^2+(del=5Fx2= )^2
> if f =3D x*y then (delf/f)^2=3D (del=5Fx/x)^2+(del=5Fy/y)^2
>
> If x1, ...xn are functions of other variables I find the general formu= la
> above (with derivatives) much easier to use.
>
> Ioana
>
> On Wed, 14 May 2003, VITORGE Pierre 094605 wrote:
>
> > d(dG) =3D square root([d(dH)]^2 + [d(dS)]^2)
> > cannot be true, if dh=3D0 and T is constant the above Eq. gives > > d(dG) =3D d(dS)
> > while it is of course
> > d(dG) =3D T d(dS)
> >
> > You probably mean:
> > d(DG) =3D square root([d(DH)]^2 + [(Td(DS)+(DS)dT)]^2)?
> > or
> > d(DG) =3D square root([d(DH)]^2 + [Td(DS)]^2 + [(DS)dT]^2)?
> >
> > Pierre Vitorge
> > CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-CNRS-Universite = d'Evry)
> > Universite d'Evry UMR 8587
> > pierre.vitorge@cea.fr
> > http://perso.club-internet.fr/vitorgen/pierre/pierre.html
> >
> >
> > -----Message d'origine-----
> > De: Dr. Richard L. Wood [mailto:rlw28@cornell.edu]
> > Date: lundi 12 mai 2003 15:58
> > =C0: Wong Lai Ho
> > Cc: CHEMISTRY@ccl.net
> > Objet: CCL:Error estimation of gibbs free energy
> >
> >
> > Wouldn't the following be true
> >
> > d(dG) =3D square root([d(dH)]^2 + [d(dS)]^2)?
> >
> > dG is delta G, d(dG) is the error in delta G, dH is delta H, d(dH= ) is
> the
> > error
> > in delta H, dS is delta S and d(dS) is the error in delta S.
> >
> > This is taken from a simple error propagation analysis as taught = in some
> > physical/analytical chemistry laboratories.
> >
> > Richard
> >
> > Wong Lai Ho wrote:
> >
> > > Dear CCLers,
> > >
> > > I have a question regarding error estimation of the experime= ntal
> values of
> > > gibbs free energy.
> > > As we knows that:
> > > delta G(formation)
> > >    =3D delta H(formation)
> > >    - Temp * [entropy(molecule)-sum(entropy(atoms t= o form the
> molecules))]
> > >
> > > Can I claim that the experimental error bar of the gibbs fre= e
> energy(delta
> > > G) is equal to the error bar of the enthalpy change of forma= tion(delta
> H)?
> > > (since the error introduced by the entropy is usually very s= mall)
> > > Is there any papers or books talking about this error?
> > >
> > > I would be grateful if you can give some comments on this cl= aim.
> > >
> > > Larry
> > >
> >
> > --
> > Richard L. Wood, Ph. D.
> > Physical/Computational Chemist
> > Post-doctoral Associate
> > Department of Chemistry
> > Trinity University, San Antonio, TX 78212
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
> -=3D This is automatically added to each message by mailing script =3D= -
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net --= To
> Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/ &nbs= p; | Jan: jkl@ccl.net
>
>
>
>
>
>
>
>


--=_alternative 0068EB6A05256D27_=-- From chemistry-request@server.ccl.net Fri May 16 03:59:13 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4G7x6J24764 for ; Fri, 16 May 2003 03:59:08 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id PAA02512 for ; Fri, 16 May 2003 15:52:48 +0800 Message-Id: <200305160752.PAA02512@mx1.ustc.edu.cn> Date: Fri, 16 May 2003 15:54:51 +0800 From: ¶¡Ñ¸À× Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: Summary: Frozen calculation in Gaussian Organization: Öйú¿Æ´óÑ¡¼ü»¯Ñ§ÊµÑéÊÒ X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon624371462114_=====" This is a multi-part message in MIME format. --=====000_Dragon624371462114_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xzo7oNCg0KCVdpdGggdGhlIGhlbHAgb2YgSmltIEhlc3MgYW5kIENoZWVycyBNYXJ0 aWpuICwgaGVyZSBhcmUgc29tZSB3YXlzIHRvDQoJZG8gZnJvemVuIGNhbGN1bGF0aW9ucyBpbiBH YXVzc2lhbi4NCgkNCiAgICAxLkZyb3ppbmcgb25lIGF0b206DQogICAgICBXcml0ZSAwIG9yIC0x IGJldHdlZW4gdGhlIGF0b20gY2VudGVyIGxhYmVsIGFuZCB0aGUgY29vcmRpbmF0ZXMuIC0xIGZv ciBmcm96ZW4gDQoJICBhbmQgMCBmb3Igbm90LWZyb3plbi5MaWtlIHRoaXM6DQoJX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX18NCgkjcmhmL3N0by0z ZyBvcHQgbm9zeW1tIHRlc3QNCg0KICAgICBzaWxseSBjaGVtaXN0cnksIGJ1dCBmb3IgaWxsdXN0 cmF0aXZlIHB1cnBvc2VzLi4uDQoNCiAgICAgMCwxDQogICAgIDggIDAgICAgICAgLTEuMDAwMDAw ICAgIDAuMDAwMDAwICAgIDAuMDAwMDAwDQogICAgIDYgLTEgICAgICAgIDAuMDAwMDAwICAgIDEu MDAwMDAwICAgIDAuMDAwMDAwDQogICAgIDYgLTEgICAgICAgIDAuMDAwMDAwICAgLTEuMDAwMDAw ICAgIDAuMDAwMDAwDQogICAgIDggIDAgICAgICAgIDEuMDAwMDAwICAgIDAuMDAwMDAwICAgIDAu MDAwMDAwDQoNCglfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX1+hoaGhDQoJDQoJMi5Gcm96aW5nIG9ubHkgc3BlY2lmaWMgY29vcmRpbmF0ZXMoZS5n LiB6LWNvb3JkaW5hdGUgb25seSkuDQogIAlVc2Ugc3ltYm9saWMgY2FydGVzaWFuIGNvb3JkaW5h dGVzIGFuZCBzZXQgIm9wdD16LW1hdHJpeCIgLg0KCVRoZSBjb29yZGluYXRlcyB0byBiZSBmcm96 ZW4gYXJlIGZsYWdnZWQgd2l0aCBhbiAiRiIgaW4gdGhlIA0KICAgICJWYXJpYWJsZXM6IiBzZWN0 aW9uLkxpa2UgdGhpczoNCglfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fDQoJI3JoZi9zdG8tM2cgb3B0PSh6LW1hdHJpeCkgdGVzdA0KDQogICAgIHN5bWJvbGljIGNh cnRlc2lhbiBvcHRpbWl6YXRpb24NCg0KCQkwLDENCgkJTzEgMCB4MSAgeTEgIHoxDQoJCUMyIDAg eDIgIHkyICB6Mg0KCQlDMyAwIHgzICB5MyAgejMNCgkJVmFyaWFibGVzOg0KCQl4MT0tMS4NCgkJ eTE9MC4NCgkJejE9MC4NCgkJeDI9MC4gDQoJCXkyPTEuIA0KCQl6Mj0wLiBGDQoJCXgzPTAuDQoJ ICAgIHkzPTEuDQoJICAgIHozPTEuIEYNCgkNCglfX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fXw0KCQ0KICAgIDMuIFVzZSBpbnRlcm5hbCBjb29yZGluYXRlcywgaW4g dGhlIGNvbnN0YW50IHNlY3Rpb24gc2V0IHRoZSBmcm96ZW4gaXRlbS4gDQoJTGlrZSB0aGlzKHRo ZSBhbmdsZSB3aWxsIGJlIGZyb3plbik6DQoJX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fXyANCgkjcmhmL3N0by0zZyBvcHQ9KHotbWF0cml4KSB0ZXN0DQoNCiAgICAg aW50ZXJuYWwgY29vcmRpbmF0ZXMNCg0KCQkwLDENCgkJQzEgDQoJCU8yICBDMSAgcjENCgkJQzMg IE8yICByMSAgQzEgYW5nbGUgDQoJCVZhcmlhYmxlczoNCgkJcjE9MS41DQoJICAgIGNvbnN0YW50 DQoJICAgIGFuZ2xlPTYwLjAgIA0KCQ0KICAgIF9fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fDQoJDQoJNC4gVXNlIE1vZFJlZHVuLiBMaWtlIHRoaXModGhlIGFuZ2xl IHdpbGwgYmUgZnJvemVuKToNCglfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX18NCgkjcmhmL3N0by0zZyBPcHQ9TW9kUmVkdW4gDQoNCglNb2RSZWR1biB0 ZXN0DQoNCgkJMCwxDQoJCUMxIA0KCQlPMiAgQzEgIHIxDQoJCUMzICBPMiAgcjEgIEMxIGFuZ2xl IA0KCQlWYXJpYWJsZXM6DQoJCXIxPTEuNQ0KCSAgICBhbmdsZT02MC4wICANCgkgICAgTW9kUmVk dW4NCiAgICAgICAgMyAyIDEgNjAuMCAgIEYNCgkNCglfX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fXw0KICAgICBPbmUgY2Fubm90IGluY2x1ZGUgZHVt bXkgYXRvbXMgYXMgcGFydCBvZiBhIGNvbnN0cmFpbmVkIGNvb3JkaW5hdGUgDQogICAgIHdoZW4g cGVyZm9ybWluZyBvcHRpbWl6YXRpb25zIGluIHJlZHVuZGFudCBpbnRlcm5hbCBjb29yZGluYXRl cy4NCg0KICAgIFRoYW5rIHlvdSBmb3IgeW91ciBoZWxwIaGhoaGhoaGhoaGhoaGhoaENCiAJCQkJ DQqhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhRGluZyBYdW5sZWkNCqGhoaGhoaGhoaGhoaGh oaGhoaGhoaGhoaGhoaEyMDAzLTA1LTE2DQpfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fDQpEaW5nIFh1bmxlaSwgUGguRC4gQ2FuZGlkYXRlDQpPcGVuIExhYm9y YXRvcnkgb2YgQm9uZCBTZWxlY3RpdmUgQ2hlbWlzdHJ5DQpVbml2ZXJzaXR5IG9mIFNjaWVuY2Ug JiBUZWNobm9sb2d5IG9mIENoaW5hDQpIZWZlaSwgQW5odWkgMjMwMDI2LCBQLlIuQ2hpbmENClRl bC46IDAwODYtNTUxLTM2MDM0MTgNCkZheC46IDAwODYtNTUxLTM2MDI5NjkNCkUtbWFpbDogZHhs QG1haWwudXN0Yy5lZHUuY24NCkh0dHA6Ly93d3cuYnNjLnVzdGMuZWR1LmNuL35keGwNCg== --=====000_Dragon624371462114_===== Content-Type: image/gif; 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Thu, 15 May 2003 23:25:42 -0400 Received: from localhost (wang@localhost) by euch4e.chem.emory.edu (AIX5.1/8.9.3/8.9.3) with ESMTP id XAA54582 for ; Thu, 15 May 2003 23:25:39 -0400 Date: Thu, 15 May 2003 23:25:33 -0400 (EDT) From: Qingfang Wang To: Subject: Energy Decomposition Analysis for strongly bonded systems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL folks, Is there any code to do some EDA analysis for system where a strong covalent bond is formed? Thanks. Qingfang Wang Department of Chemistry Emory University Tel 4047272381 From chemistry-request@server.ccl.net Thu May 15 18:23:39 2003 Received: from kuma.unm.edu ([129.24.9.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4FMNdJ27041 for ; Thu, 15 May 2003 18:23:39 -0400 Received: (qmail 22767 invoked by uid 124); 15 May 2003 16:23:37 -0600 Received: from cabaniss@unm.edu by mail.unm.edu by uid 121 with qmail-scanner-1.16 (csav: version 4.75.1 deffiles-20030512 Clear:. Processed in 0.271089 secs); 15 May 2003 22:23:37 -0000 Received: from dhcp-40-1003.unm.edu (HELO unm.edu) (129.24.47.238) by kuma.unm.edu with SMTP; 15 May 2003 16:23:37 -0600 Message-ID: <3EC41350.4000905@unm.edu> Date: Thu, 15 May 2003 16:23:12 -0600 From: Steve Cabaniss User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:0.9.4.1) Gecko/20020508 Netscape6/6.2.3 X-Accept-Language: en-us MIME-Version: 1.0 To: Ioana Cozmuta CC: WU_GUOSHENG@Lilly.com, CHEMISTRY@ccl.net Subject: Error estimation of gibbs free energy References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Ioana & Guosheng- This derivation is commonly given in quantitative analysis texts in abbreviated form. Another reference for a more thorough version is in "Data Reduction and Error Analysis for the Physical Sciences" 2nd. edition, by PR Bevington and DK Robinson. Steve Ioana Cozmuta wrote: > Hi Guosheng, > > >>From the top of my head, that formula comes from a Taylor expansion in >> > which you neglect the higher-order terms. > > Honestly, the best info I have on error propagation are my hand written > notes from the courses I followed during undergrad/grad studies. > However, if you do a search on google with the following terms: > general formula error propagation > it gives lots of references. > The most frequently mentioned reference I see is > Taylor, J. R., "An introduction to Error Analysis", University Science > Books, 1982. > I also think that any book on numerical analysis should have at least a > chapter that covers error propagation. > See also: > http://mulliken.chem.hope.edu/~polik/Chem345-2000/errorpropagation.htm > > Regards, > Ioana > > **************************************************************************** > * Ioana Cozmuta, PhD * * > * NASA-AMES Research Center * "Gravitation can not be held responsible* > * Mail Stop 230-3 * for people falling in love" * > * Moffet Field,CA 94035 * * > * phone: (650) 604-0993 * Albert Einstein* > * fax: (650) 604-0350 * (1879-1955) * > **************************************************************************** > > On Thu, 15 May 2003 WU_GUOSHENG@Lilly.com wrote: > > >>Dear Ioana, >> >>Could you please point out if there is any reference for your equation? -- Steve Cabaniss Professor, Environmental and Analytical Chemistry Dept. of Chemistry University of New Mexico Albuquerque, NM 87131 Voice (505) 277-4445 FAX 277-2609 From chemistry-request@server.ccl.net Fri May 16 02:59:16 2003 Received: from turmiel.ch.uj.edu.pl ([149.156.71.252]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4G6xFJ20853 for ; Fri, 16 May 2003 02:59:16 -0400 Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.11.6/8.11.6) id h4G6xBP05320; Fri, 16 May 2003 08:59:11 +0200 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to makowskm@chemia.uj.edu.pl using -f Received: from 149.156.71.133 (SquirrelMail authenticated user makowskm) by mail.ch.uj.edu.pl with HTTP; Fri, 16 May 2003 08:59:11 +0200 (CEST) Message-ID: <1548.149.156.71.133.1053068351.squirrel@mail.ch.uj.edu.pl> Date: Fri, 16 May 2003 08:59:11 +0200 (CEST) Subject: SAC-CI in Gaussian03 From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit Dear CCLers, I have a problem with using SAC-CI method included in Gaussian03 suite. I am interested in geometry optimization of the ground state using this method, but until now all of my tries of preparing an appropriate input failed. My input looked like this: %chk=/tmp1/ucmakows/benosnz_sac #P SAC-CI(SACOnly)/cc-pVDZ opt GFinput IOP(6/7=3) Guess(Read) Geom=AllCheck where checkpoint file is from previous RHF optimization It resulted in: Must specify TargetState for gradients. Error termination via Lnk1e in /usr_ext1/gaussian03/g03/l923.exe at Thu May 15 16:46:24 2003. Job cpu time: 0 days 0 hours 32 minutes 4.5 seconds. File lengths (MBytes): RWF= 7059 Int= 0 D2E= 0 Chk= 8 Scr= 1 > From my previous experiments it looked like that TargetState option is addressed to excited states not a ground(reference) one. May anyone give any suggestion what the route section should be? Thanks in advance, -- Marcin Makowski Ph.D. student in Theoretical Chemistry, Jagellonian University From chemistry-request@server.ccl.net Thu May 15 20:39:10 2003 Received: from web20608.mail.yahoo.com ([216.136.226.166]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4G0dAJ31743 for ; Thu, 15 May 2003 20:39:10 -0400 Message-ID: <20030516003854.3602.qmail@web20608.mail.yahoo.com> Received: from [206.111.112.115] by web20608.mail.yahoo.com via HTTP; Thu, 15 May 2003 17:38:54 PDT Date: Thu, 15 May 2003 17:38:54 -0700 (PDT) From: Sengen Sun Subject: A question on SC WFs To: chemistry@ccl.net Cc: pbkl@york.ac.uk MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL members, I have some confusion about spin-coupled valance-bond wave functions, as used by Professor Peter Karadakov in the description of Diels-Alder reactions and 1,3-dipolar cycloadditions (JPC A 2003, 107, 2548; and refs therein). I am still trying to understand how the change of SC WFs along IRC means the relocating event of electrons. I don’t have any hands-on experience of the SC WF calculations. I hope that some body can come forward to clarify this. I believe that many people are interested in this issue. The problem in my mind is Richard Bader’s notion that any sub-quantum system is an open system. I can not accept both Bader’s notion and Karadakov’s theory in the same time. If I accept one, I must reject the other, because they are philosophically conflicting. Is anything wrong with my thinking? For some new members on this list, please see my detailed discussions on the related issues: http://preprint.chemweb.com/orgchem/0201002 Playing the Natural Puzzles of Concerted Cycloadditions: What Are the Tricks behind the Scene? http://preprint.chemweb.com/orgchem/0107002 Collision-induced electron reorganization as the general mechanism of concerted cycloaddition reactions. (A Tetrahedron referee on this paper urged me to use Valance-Bond Theory to address what I was concerned with. I am trying to, but I don’t know how). http://preprint.chemweb.com/orgchem/0210002, Natural forces as the foundation of theoretical explanations in organic chemistry. http://www.ccl.net/cgi-bin/ccl/message.cgi?2002+04+06+004 Cheers! __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com From chemistry-request@server.ccl.net Fri May 16 02:20:01 2003 Received: from web12303.mail.yahoo.com ([216.136.173.101]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4G6K0J18278 for ; Fri, 16 May 2003 02:20:00 -0400 Message-ID: <20030516062000.22755.qmail@web12303.mail.yahoo.com> Received: from [202.141.70.12] by web12303.mail.yahoo.com via HTTP; Thu, 15 May 2003 23:20:00 PDT Date: Thu, 15 May 2003 23:20:00 -0700 (PDT) From: Anirban Subject: CCL:DLPOLY(free boundary condition) To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi ! I would like to know if anybody has done implemented free boundary condition for water clusters using DLPOLY package or not . I have been trying to implement it using the package. When I try to restart a particular run for water cluster it gives error saying "mxlist(Verlet neighbour list array) too small". Could someone suggest what should I do ? What all things I need to take care of for doing a molecular dynamics simulations for water clusters using DLPOLY package. In other words what all directives the "CONTROL" file should have ? Thanx in advance ! anirban __________________________________ Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. http://search.yahoo.com From chemistry-request@server.ccl.net Fri May 16 17:07:34 2003 Received: from chem.umn.edu ([128.101.157.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4GL7XJ22618 for ; Fri, 16 May 2003 17:07:34 -0400 Received: (qmail 67643 invoked from network); 16 May 2003 21:07:33 -0000 Received: from unknown (HELO chem.umn.edu) (128.101.156.132) by 0 with SMTP; 16 May 2003 21:07:33 -0000 Message-ID: <3EC55315.8080402@chem.umn.edu> Date: Fri, 16 May 2003 16:07:33 -0500 From: Jiali Gao User-Agent: Mozilla/5.0 (Macintosh; U; PPC Mac OS X; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: Qingfang Wang CC: chemistry@ccl.net Subject: Re: CCL:Energy Decomposition Analysis for strongly bonded systems References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Qingfang, You may find a couple of papers that Professor Yirong Mo and I published to be relevant to your question. The references are: 1. Y. Mo, Y. Zhang, J. Gao, "A Simple Electrostatic Model for Trisilylamine: Theoretical Examinations of the n? s* Negative Hyperconjugation, p p?pd Bonding, and Stereoelectronic Interaction." Journal of the American Chemical Society, 1999, 121, 5737-5742. 1. Y. Mo, J. Gao, S. D. Peyerimhoff, "Energy Decomposition Analysis of Intermolecular Interactions using a Block-localized Wavefunction Approach." Journal of Chemical Physics , 2000, 112, 5530-5538. 1. Y. Mo, J. Gao, "Polarization and Charge-Transfer Effects in Lewis Acid-Base Complexes." Journal of Physical Chemistry, 2001, 105, 6530-6536. The last two papers include examples that have significant covalent character for which other energy decomposition methods fail completely especially when large basis sets are used. Jiali Gao Qingfang Wang wrote: >Dear CCL folks, > >Is there any code to do some EDA analysis for system where a strong >covalent bond is formed? Thanks. > >Qingfang Wang >Department of Chemistry >Emory University >Tel 4047272381 > > > > > >-= 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 > > > > > > >. > -- ------------------------------------------------------------------- Jiali Gao Department of Chemistry and Digital Technology Center University of Minnesota, Minneapolis, MN 55455 gao@chem.umn.edu, phone: 612-625-0769, fax: 612-626-7541 http://vesta.chem.umn.edu DGS, Scientific Computation Graduate Program http://www.scicomp.umn.edu ------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 16 12:38:03 2003 Received: from mail.ncifcrf.gov ([129.43.100.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4GGc2J02046 for ; Fri, 16 May 2003 12:38:02 -0400 Received: from S048990 ([129.43.22.69]) by mail.ncifcrf.gov (8.11.3/8.11.3) with ESMTP id h4GGbkR16745 for ; Fri, 16 May 2003 12:37:57 -0400 (EDT) Message-Id: <4.2.0.58.20030516123617.01342b18@mail.ncifcrf.gov> X-Sender: cfrankenberger@mail.ncifcrf.gov (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Fri, 16 May 2003 12:37:28 -0400 To: chemistry@ccl.net From: Casey Frankenberger Subject: EST to protein structure Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello Everyone, I am a beginner at structural biology projects and I have just been given the task of trying to find a theoretical structure of proteins corresponding to 2 different ESTs. I wanted to explain the method I was going to follow and see if any of you could give me suggestions as to pitfalls in my methodology or better/more efficient techniques to use. First I was going to find the sequences of the ESTs translate them to the amino sequence, then BLAST them to find similar sequences in hopes that one or some of them will have a structure solved already. If so Ill use this as a model. Other wise Ill try to find a software to simulate the protein folding of the sequence although I ve heard this is sometimes very inaccurate. Hopefully Ill learn alot from this exercise and your all's suggestions. Thanks Casey frankenberger LMT NCI-Frederick From chemistry-request@server.ccl.net Fri May 16 09:19:07 2003 Received: from portia.cc.emory.edu ([170.140.204.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4GDJ7J24990 for ; Fri, 16 May 2003 09:19:07 -0400 Received: from emory.edu (localhost [127.0.0.1]) by portia.cc.emory.edu (8.12.9/8.12.9) with ESMTP id h4GDJ7cb027713 for ; Fri, 16 May 2003 09:19:07 -0400 (EDT) Date: Thu, 15 May 2003 23:06:56 -0400 Content-Type: text/plain; charset=US-ASCII; format=flowed Resent-Date: Fri, 16 May 2003 09:21:36 -0400 Content-Transfer-Encoding: 7bit Resent-Message-Id: <73A222C1-874B-11D7-901D-000A95680A26@emory.edu> Resent-To: chemistry@ccl.net Mime-Version: 1.0 (Apple Message framework v552) Subject: question about freq reordering in POLYRATE From: Qingfang Wang To: chemistry@ccl.net Message-Id: <52198D4E-87A1-11D7-901D-000A95680A26@emory.edu> Resent-From: Qingfang Wang X-Mailer: Apple Mail (2.552) Dear CCL folks, To calculate the Small Curvature Tunneling corrections I need to reordering the vibrational frequency along the MEP. For my reaction system containing 5 atoms and in C1 symmetry, it is hard to identify the nature of vibrational modes by investigating the vibration vectors or by visualize them. Is there any systematic way to do such job? Any suggestions or literature references will be greatly appreciated. Qingfang Wang Department of Chemistry Emory University Atlanta Ga 30322 Tel: 4047272381 From chemistry-request@server.ccl.net Fri May 16 07:24:55 2003 Received: from ukpweb02.inha.ac.kr ([165.246.16.155]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4GBOsJ22154 for ; Fri, 16 May 2003 07:24:54 -0400 Received: from TEST ([165.246.154.97]) by ukpweb02.inha.ac.kr with Microsoft SMTPSVC(5.0.2195.5329); Fri, 16 May 2003 20:23:33 +0900 Message-ID: <000c01c31b9e$3687ad70$619af6a5@TEST> From: "Prof. Chan Kyung Kim" To: Subject: electronic energy of H- Date: Fri, 16 May 2003 20:28:02 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C31BE9.A6682980" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-OriginalArrivalTime: 16 May 2003 11:23:33.0701 (UTC) FILETIME=[96019F50:01C31B9D] This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C31BE9.A6682980 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 RGVhciBjb21wdXRhdGlvbmFsIGNoZW1pc3RzOg0KDQogICAgSSBhbSBsb29raW5nIGZvciB0aGUg dGhlIGV4cGVyaW1lbnRhbCBlbGVjdHJvbmljIGVuZXJneSBvZiBILSBpb24oaHlkcmlkZSBpb24p LiBBbnkgcmVmZXJlbmNlPyANCg0KVGhhbmtzIGluIGFkdmFuY2UuDQoNCkNoYW4uDQo9PT09PT09 PT09PT09PT09PT09PT0NClByb2YuIENoYW4gS3l1bmcgS2ltDQpEZXBhcnRtZW50IG9mIENoZW1p c3RyeQ0KSW5oYSBVbml2ZXJzaXR5DQpJbmNob24sIDQwMi03NTEsIEtvcmVhDQooVGVsKSArODIt MzItODYwLTc2ODQNCihGYXgpICs4Mi0zMi04NjctNTYwNA0KKGVtYWlsKSBrY2t5dW5nQGluaGEu YWMua3I= ------=_NextPart_000_0009_01C31BE9.A6682980 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWtzX2NfNTYwMS0xOTg3Ij4NCjxNRVRBIGNvbnRlbnQ9Ik1T SFRNTCA2LjAwLjI4MDAuMTEwNiIgbmFtZT1HRU5FUkFUT1I+DQo8U1RZTEU+PC9TVFlMRT4NCjwv SEVBRD4NCjxCT0RZIGJnQ29sb3I9I2ZmZmZmZj4NCjxESVY+PEZPTlQgc2l6ZT0yPkRlYXIgY29t cHV0YXRpb25hbCBjaGVtaXN0czo8L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIHNpemU9Mj48L0ZP TlQ+Jm5ic3A7PC9ESVY+DQo8RElWPjxGT05UIHNpemU9Mj4mbmJzcDsmbmJzcDsmbmJzcDsmbmJz cDtJIGFtIGxvb2tpbmcgZm9yIHRoZSZuYnNwO3RoZSANCmV4cGVyaW1lbnRhbCBlbGVjdHJvbmlj IGVuZXJneSBvZiBILSBpb24oaHlkcmlkZSBpb24pLiBBbnkgcmVmZXJlbmNlPyANCjwvRk9OVD48 L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQg c2l6ZT0yPlRoYW5rcyBpbiBhZHZhbmNlLjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0y PjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0yPkNoYW4uPC9GT05UPjwvRElW Pg0KPERJVj48Rk9OVCBzaXplPTI+PT09PT09PT09PT09PT09PT09PT09PEJSPlByb2YuIENoYW4g S3l1bmcgS2ltPEJSPkRlcGFydG1lbnQgb2YgDQpDaGVtaXN0cnk8QlI+SW5oYSBVbml2ZXJzaXR5 PEJSPkluY2hvbiwgNDAyLTc1MSwgS29yZWE8QlI+KFRlbCkgDQorODItMzItODYwLTc2ODQ8QlI+ KEZheCkgKzgyLTMyLTg2Ny01NjA0PEJSPihlbWFpbCkgPEEgDQpocmVmPSJtYWlsdG86a2NreXVu Z0BpbmhhLmFjLmtyIj5rY2t5dW5nQGluaGEuYWMua3I8L0E+PC9GT05UPjwvRElWPjwvQk9EWT48 L0hUTUw+DQo= ------=_NextPart_000_0009_01C31BE9.A6682980-- From chemistry-request@server.ccl.net Fri May 16 13:00:03 2003 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4GH02J04010 for ; Fri, 16 May 2003 13:00:02 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Fri, 16 May 2003 14:02:11 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B32@correio.cetem.gov.br> From: Ian Hovell To: "'Constanza Cardenas'" , CHEMISTRY@ccl.net Subject: RE: HELP: 2GB Scratch file limit in G98 on Linux/i386 Date: Fri, 16 May 2003 14:02:10 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4GH03J04011 I came accross this a few weeks back. In the route section you can insert information that tells gaussian to split the rwf scratch file into smaller sizes. I.e. %rwf=a.rwf,200MW,b.rwf,200MW,c.rwf,200MW etc. This will split the rwf file into three files each of 200MW size or 200*8000 approx.bytes. I have found that you can create upto 7 files in this way. I have read somewhere that you can create 8 but on doing so I have found that gaussian starts to misbehave. I hope this helps. Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Ciência e da Tecnologia- MCT Avenida Ipê, No 900 - Cidade Universitaria Ilha do Fundão Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell@cetem.gov.br -----Original Message----- From: Constanza Cardenas [SMTP:conscc@yahoo.com] Sent: Wednesday, May 14, 2003 1:18 PM To: CHEMISTRY@ccl.net Subject: CCL:HELP: 2GB Scratch file limit in G98 on Linux/i386 Dear CClers- We are using G98 Rev A.11 compiled with gcc-2.96 (linux/i386 2.4.18). However, the scatch files cannot grow beyond a 2GB limit. Apparently, SEEK uses 32 bit integers and this causes the file size limit. How have any of you overcome this scratch file size limit? TIA, Constanza _________________________________________________________ Do You Yahoo!? Información de Estados Unidos y América Latina, en Yahoo! Noticias. Visítanos en http://noticias.espanol.yahoo.com -= 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 Fri May 16 18:12:42 2003 Received: from col-msxproto1.col.missouri.edu ([128.206.3.151]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h4GMCgJ29643 for ; Fri, 16 May 2003 18:12:42 -0400 Received: from [128.206.98.89] ([128.206.98.89]) by col-msxproto1.col.missouri.edu over TLS secured channel with Microsoft SMTPSVC(5.0.2195.6673); Fri, 16 May 2003 17:12:41 -0500 Mime-Version: 1.0 X-Sender: HarrisR@pop.missouri.edu Message-Id: In-Reply-To: References: Date: Fri, 16 May 2003 17:12:41 -0500 To: Ioana Cozmuta , From: "Robert E. Harris" Subject: Re: CCL:Error estimation of gibbs free energy Cc: CHEMISTRY@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-OriginalArrivalTime: 16 May 2003 22:12:41.0817 (UTC) FILETIME=[44E47C90:01C31BF8] The reference that Iona supplied, http://mulliken.chem.hope.edu/~polik/Chem345-2000/errorpropagation.htm is very nice. One can make some extensions of this, and a much less nice example of discussion of this subject is located at http://www.chem.missouri.edu/chem234/ses.pdf See especially pp. 4 and 5. Near the bottom of p. 5 is what I think is sometimes a useful way of simplifying the calculations. -- Robert E. Harris Phone: 573-882-3274. Fax: 573-882-2754 Department of Chemistry, University of Missouri-Columbia Columbia, Missouri, USA 65211 From chemistry-request@server.ccl.net Fri May 16 19:37:41 2003 Received: from oehehyr ([218.224.36.85]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h4GNbdJ02552 for ; Fri, 16 May 2003 19:37:40 -0400 From: Antonia Pue-Gilchrist To: Subject: In the News 2002 Date: Fri, 16 May 2003 15:40:18 -0700 Mime-Version: 1.0 Content-Type: text/html Message-Id:
This will help.
Do it for her.





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