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To: chemistry@ccl.net
From: Christoph van =?iso-8859-1?Q?W=FCllen?=  <Christoph.vanWullen@tu-berlin.de>
Subject: Gaussian Makefile War
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Let me add to this odd discussion that users who can not apply 
trivial changes to the Makefile themselves, should really stick to 
out-of-the-box versions.
For, if something goes wrong (and suspicious numbers are produced), the are
alone in the dark.
Let me remind you that most ports to "unsupported" platforms even include
some hacking in the source code (esp. mdutil), if I remember correctly, the
g77 version required such things. So, this particular adaption from pgf to
ifc cannot be that hard.

From chemistry-request@server.ccl.net Tue Dec 11 02:59:26 2001
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Date: Tue, 11 Dec 2001 15:58:29 +0800 (CST)
From: =?gb2312?q?yong=20pei?= <ypnju@yahoo.com.cn>
Subject: MD at constant energy .
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Dear Sir

I have a question about the molecular dynamics
simulation .When I carry out dynamics simulation at
constant energy ,how can I determine the
equillibration of the system? 

Regards

Yong Pei
Deparment of Chemsitry
NanJing University
P. R. China   


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From chemistry-request@server.ccl.net Tue Dec 11 04:07:19 2001
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To: CCL mailing list <CHEMISTRY@ccl.net>
Subject: Re: Gaussian 98 makefile policy
References: <200112102236.RAA54325@svega.gaussian.com>
From: Andrey Khavryuchenko <akhavr@kds.com.ua>
Organization: KDS Software Group
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Mike,

"MF" == Mike Frisch wrote:

 MF> I'm suggesting that without proper testing, one should reserve judgement.
 MF> As is typical for such things, in this case, there isn't even a claim made
 MF> that the entire test suite has been run, or that the answers have been
 MF> carefully checked.  It would be extremely unusual for a build with a new
 MF> compiler to work on the whole test suite the first time, without a single
 MF> routine needing reduced optimization due to compiler problems.

So why not provide this test suite to the person that made a change in
Makefile and bless to release it only when all tests pass?

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

From chemistry-request@server.ccl.net Tue Dec 11 04:12:08 2001
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To: chemistry@ccl.net
Subject: Re: CCL:Gaussian 98 benchmark for PC systems 
In-reply-to: Your message of "Sat, 08 Dec 2001 23:22:15 +0800."
             <20011208232215.A10603@OXYGEN.chem.nthu.edu.tw> 
Date: Tue, 11 Dec 2001 10:11:50 +0100
From: Malcolm Gillies <malcolm@kemi.dtu.dk>
Message-Id: <E16Dix4-00044O-00@ouabain.ok.dtu.dk>

> 	We have got the information from Gaussian Inc. that distributing the
> modified version of makefile or the instructions is violation to the licence
> agreement.

Maybe I'm being obtuse, but posting a patch (i.e. a diff) to the Gaussian
makefile would seem the obvious solution. This way you do not have to
distribute the Gaussian-licensed code.

There is a patch available to make g98 compile with the g77 compiler,
for instance:

    http://quanta.synchem.kyoto-u.ac.jp/~maho/Computer/Linux_gaussian_e.html

Preparing the patch is just a matter of

    diff -c makefile.old makefile.new >g98.patch

or something similar...

cheers,

Malcolm
--
Malcolm Gillies <malcolm.gillies@kemi.dtu.dk>
Post-doctoral researcher
Organic Chemistry, Dept Chemistry,
Technical University of Denmark

From chemistry-request@server.ccl.net Tue Dec 11 06:30:17 2001
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From: "nahoko matsuzawa" <nahoko@nandomail.com>
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Date: Tue, 11 Dec 2001 03:23:00 -0800
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Subject: fixing angle in MD (GROMACS)
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Dear all,

I wish to use GROMACS to simulate some polymers.  I want
to fix the bond lengths as well as the bond angles.  Taking
only the LJ, charge and dihedral into account.  

It seems that using SHAKE one can fix the bond length easily
(just add a line in the constrain).  Is it true that when
I want to fix the bond angle I should fix the distance between
the 1-3 atoms which define the bond angle?  

I think carefully and it looks like it would work.  Beside in
the water .itp they fixed the angle by constraning the H-H 
distance.  I am just curious whether there is a more elegant 
way of constraining the angle.

thanks in advance
nahoko

________________________________________________________________
To get your free Web-based E-mail go to http://www.nandomail.com

From chemistry-request@server.ccl.net Tue Dec 11 06:43:44 2001
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From: "JinhyukLee" <mack@statchem.snu.ac.kr>
To: "ccl ccl" <chemistry@ccl.net>
Subject: QM/MM example input file in CHARMM
Date: Tue, 11 Dec 2001 20:42:33 +0900
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Hello Cclers

I'd like to obtain the information of a QM/MM example input file in CHARMM. My CHARMM (27b3) has a few testcase for QM/MM. In particular, a QM/MM, using the GAMESS, is better.

Have a nice day. Thx in advance for ur helps.

--
JinhyukLee

From chemistry-request@server.ccl.net Tue Dec 11 06:48:10 2001
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From: David van der Spoel <spoel@xray.bmc.uu.se>
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To: nahoko matsuzawa <nahoko@nandomail.com>
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Subject: Re: CCL:fixing angle in MD (GROMACS)
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On Tue, 11 Dec 2001, nahoko matsuzawa wrote:

>Dear all,
>
>I wish to use GROMACS to simulate some polymers.  I want
>to fix the bond lengths as well as the bond angles.  Taking
>only the LJ, charge and dihedral into account.
>
>It seems that using SHAKE one can fix the bond length easily
>(just add a line in the constrain).  Is it true that when
>I want to fix the bond angle I should fix the distance between
>the 1-3 atoms which define the bond angle?
>
>I think carefully and it looks like it would work.  Beside in
>the water .itp they fixed the angle by constraning the H-H
>distance.  I am just curious whether there is a more elegant
>way of constraining the angle.
set in the mdp file
constraints = all-angles
constraint-algorithm     = shake

>thanks in advance
>nahoko
>
>________________________________________________________________
>To get your free Web-based E-mail go to http://www.nandomail.com
>
>-= This is automatically added to each message by mailing script =-
>CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
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>
>
>

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel@xray.bmc.uu.se	spoel@gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From chemistry-request@server.ccl.net Tue Dec 11 07:08:45 2001
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From: "JinhyukLee" <mack@statchem.snu.ac.kr>
To: "ccl ccl" <chemistry@ccl.net>
Subject: QCMD(Quantum Classical Molecular Dynamics) source code?
Date: Tue, 11 Dec 2001 21:07:34 +0900
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Hi Cclers,

One more question.. Isn't there anyone who has source code of QCMD? 

Have a nice day

__
JinhyukLee

From chemistry-request@server.ccl.net Tue Dec 11 08:25:56 2001
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Date: Tue, 11 Dec 2001 12:19:03 +0000
From: Laurence Cuffe <Laurence.Cuffe@ucd.ie>
Subject: Re: CCL:Gaussian 98 makefile policy
In-reply-to: <200112102003.PAA99052@svega.gaussian.com>
To: frisch@gaussian.com (Mike Frisch), chemistry@ccl.net
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Date sent:      	Mon, 10 Dec 2001 15:03:25 -0500 (EST)
From:           	frisch@gaussian.com (Mike Frisch)
Subject:        	CCL:Gaussian 98 makefile policy
To:             	chemistry@ccl.net

>This is not a fair statement of our policy.  We provide source code, which
>few other vendors do, and makefiles for supported platforms and compilers.
>We have a careful testing procedure to help ensure that the program is
>fully and correctly functional with the supported configurations.
I think this is a tremendous advantage to the gaussian suite of 
programs, and should not be taken likely.

  Gaussian distribute the source code, the makefiles and a very 
comprehensive test suite.  It is too easy for people to alter the 
makefile until they get the program to compile and then stop right 
there without doing any further testing.

Gaussians explanation of why they don't want unauthorised 
versions of the makfile distributed makes total sense to me now 
that its been explained and should, I think, be respected.
All the best
Laurence Cuffe
>
>People can do what they want locally to make things run on on other systems,
>but passing around makefiles for unsupported platforms which have not been
>subject to careful testing is not helpful to users and also technical support
>more difficult for us.  We originally started to forbid this after a number
>of problems occurred with people unknowingly using unreliable and incorrect
>versions.  In this particular case, where there is a carefully tested and
>supported version (makefile and compiler), I think most users are much better
>off using it.


From chemistry-request@server.ccl.net Tue Dec 11 06:25:13 2001
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Organization:  
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From: "temper" <temper@chem.auth.gr>
To: <chemistry@ccl.net>
Subject: Ru (ZINDO/1_ZINDO/s)
Date: Tue, 11 Dec 2001 13:22:15 +0200
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Does anyone have ZINDO/1, ZINDO/s parameters or references where
 parameters may be found for Ru?
Thanks in advance.


Postgraduate (Ph.D) Student
Vasilios I. Teberekidis
Laboratory of Applied Quantum Chemistry=20
Aristotle University of Thessaloniki (Greece)
Tel.:(+30 31) 99 78 20
        +30937 66 18 18
E-mail: temper@chem.auth.gr
www: http://users.auth.gr/temper

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-7">
<META content=3D"MSHTML 5.50.4134.600" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3D"Comic Sans MS">Does anyone have&nbsp;ZINDO/1,=20
ZINDO/s&nbsp;parameters or references where</FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS">&nbsp;parameters </FONT><FONT=20
face=3D"Comic Sans MS">may be found </FONT><FONT face=3D"Comic Sans =
MS">for=20
Ru?</FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS">Thanks in advance.</FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2>Postgraduate (Ph.D) =
Student<BR>Vasilios=20
I. Teberekidis<BR>Laboratory of Applied Quantum Chemistry <BR>Aristotle=20
University of Thessaloniki (Greece)<BR>Tel.:(+30 31) 99 78=20
20<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +30937 66 18 =
18<BR>E-mail: <A=20
href=3D"mailto:temper@chem.auth.gr">temper@chem.auth.gr</A><BR>www: <A=20
href=3D"http://users.auth.gr/temper">http://users.auth.gr/temper</A></FON=
T></DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Tue Dec 11 09:14:12 2001
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To: "M. Nicklaus" <mn1@helix.nih.gov>
CC: chemistry@ccl.net
Subject: Re: CCL:Gaussian 98 makefile policy
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I think Marc has a good point, but also recognize that it does take a certain
man-power commitment on all concerned.

In addition, there is something for everyone here:  The Intel X86 Linux compiler
is free, if support is not needed....  and is tuned for the various Intel
hardware...

John McKelvey


"M. Nicklaus" wrote:

> On Mon, 10 Dec 2001, Mike Frisch wrote:
>
> > This is not a fair statement of our policy.  We provide source code, which
> > few other vendors do, and makefiles for supported platforms and compilers.
> > We have a careful testing procedure to help ensure that the program is
> > fully and correctly functional with the supported configurations.
>
> To satisfy both sides: Why not work closely together with this particular
> user, who seems to have done a lot of the work already, and go through the
> testing and validation procedure for this compiler/makefile/hardware
> combination to produce an official version that can be released to the
> user community as an alternative to the standard compilation?  I am sure
> that many people who are trying out alternative makefiles would be happy
> to run the necessary test jobs and evaluation procedures to produce the
> official Gaussian "blessing" in collaboration with Gaussian, Inc.,
> and if clearly told how to do so (we've offered this in the past...).
>
> Marc
>
> ------------------------------------------------------------------------
>  Marc C. Nicklaus, Ph.D.                 NIH/NCI at Frederick
>  E-mail: mn1@helix.nih.gov               Bldg 376, Rm 207
>  Phone:  (301) 846-5903                  376 Boyles Street
>  Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
>           Head, Computer-Aided Drug Design MiniCore Facility
>      Laboratory of Medicinal Chemistry, Center for Cancer Research,
>  National Cancer Institute at Frederick, National Institutes of Health
>        http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
> ------------------------------------------------------------------------
>
> -= This is automatically added to each message by mailing script =-
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From chemistry-request@server.ccl.net Tue Dec 11 08:41:26 2001
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From: "Sergio Manzetti" <sergio@proinformatix.com>
To: <chemistry@ccl.net>
Subject: XMGRACE for Windows
Date: Tue, 11 Dec 2001 14:45:22 +0100
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Dear CCLers. I am looking for XMGRACE to plot graphs for Windows, but
haven=92t got any luck in finding it.
=20
Does anyone know where it can be found?


=20
Best regards
=20
Sergio
=20
=20

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style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Dear <span =
class=3DSpellE>CCLers</span>.
I am looking for <span class=3DSpellE>XMGRACE</span> to plot graphs for =
Windows,
but haven=92t got any luck in finding it.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
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style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Does anyone know where =
it can
be found?<o:p></o:p></span></font></p>

<font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:10.0pt;font-family:
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></font></p>

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style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Best =
regards<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
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From chemistry-request@server.ccl.net Tue Dec 11 11:10:39 2001
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To: temper <temper@chem.auth.gr>
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Subject: Re: CCL:Ru (ZINDO/1_ZINDO/s)
In-Reply-To: <002701c18236$16e4e8f0$5e40cf9b@chem.auth.gr>
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> Does anyone have ZINDO/1, ZINDO/s parameters or references where
>  parameters may be found for Ru?
> Thanks in advance.

Ru ZINDO/1:

Anderson, W. P.; Cundari, T. R.; Zerner, M. C. Int. J. Quantum
Chem. 1991, vol.39, 31.

see also: Coord. Chem. Rev. 1998, vol.174, 469.

Ru ZINDO/S:

Krogh-Jespersen, K.; Westbrook, J. D.; Potenza, J. A.; Schugar, H.
J. J. Am. Chem. Soc. 1987, 109, 7025.

________________________________________________________________

                        S. I. Gorelsky
          Department  of  Chemistry,  York University
          4700 Keele Street, Toronto, Ontario M3J 1P3
          Canada

          Phone: 416-736-2100 ext#70131
          Fax:   416-736-5936
                http://www.chem.yorku.ca/grad/SG/
________________________________________________________________


From chemistry-request@server.ccl.net Tue Dec 11 10:47:41 2001
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Date: Tue, 11 Dec 2001 10:41:53 -0500
From: Rick Venable <rvenable@gandalf.cber.nih.gov>
To: =?gb2312?q?yong=20pei?= <ypnju@yahoo.com.cn>
cc: chemistry@ccl.net
Subject: Re: CCL:MD at constant energy .
In-Reply-To: <20011211075829.14453.qmail@web15001.mail.bjs.yahoo.com>
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On Tue, 11 Dec 2001, [gb2312] yong pei wrote:
> I have a question about the molecular dynamics
> simulation .When I carry out dynamics simulation at
> constant energy ,how can I determine the
> equillibration of the system? 

The general answer is to monitor the potential energy; it may have some
initial drift, but should reach a plateau once the system is
equilibrated.  The total energy (kinetic + potential) should be flat,
except for integration steps where velocities may be scaled for heating
and/or temperature equilibration during initial dynamics.

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable
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
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=




From chemistry-request@server.ccl.net Tue Dec 11 11:08:21 2001
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Hi CCL'er

With all my respect, and sorry for my bad english.

I think Gaussian is a great tool, but it has a LOT of little secrets and
"bugs", and the support is not so good, I don't think the spend that much money
on customer support, given the price of the product.

With that in mind, it's so unfair that Gaussian doesnt have a more open policy
to allow end users to comunicate improvments, or new ideas specially for new
compilers and boxes.

I have to say that from like 10 questions that I have asked to the gaussian
team support, like 2 have been answered, and those were the "easy"-well-know
ones, and they were answered when I finally asked here at CCL list. So, you
guys dont go saying that your support is so good.

Finally, would be easy to ask customers to give details about the compiling,
plataform, etc when they ask a quesion?, give an alert like : If you didn't
used our supported compiler we cannot give you good support, try a supported
compiler !!

Thanks

Max




From chemistry-request@server.ccl.net Tue Dec 11 10:58:16 2001
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From: David van der Spoel <spoel@xray.bmc.uu.se>
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To: Sergio Manzetti <sergio@proinformatix.com>
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Subject: Re: CCL:XMGRACE for Windows
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On Tue, 11 Dec 2001, Sergio Manzetti wrote:

>Dear CCLers. I am looking for XMGRACE to plot graphs for Windows, but
>haven抰 got any luck in finding it.
>
>Does anyone know where it can be found?
>
http://plasma-gate.weizmann.ac.il/Grace/

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel@xray.bmc.uu.se	spoel@gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From chemistry-request@server.ccl.net Tue Dec 11 12:25:51 2001
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Date: Tue, 11 Dec 2001 14:25:31 -0300 (GRNLNDST)
From: Jorge Gancheff <jorge@bilbo.edu.uy>
To: chemistry@ccl.net
Subject: SCIPCM problems with transition metals compounds
Message-ID: <Pine.A32.3.96.1011211140741.27064A-100000@bilbo.edu.uy>
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Dear CCLers:

I磎 trying to do an optimization and frequency calculation on 
dioxocomplexes of Re(V) with amines as ligands with the SCIPCM
(b3lyp/pseudopotential level of calculation) methodology (solvent=water),
using Gaussian 98 and an integration grid 99302.

The Gaussian package aborted the calculation giving this message:

 Cycle   2  Pass 1  IDiag 1:
 Compute SCI-PCM surface.
 WARNING!  Serious error in surface integrals.
 It is probable that some of the solute is outside the cavity and/or parts
 of the cavity 
 surface cannot be reached from the origin.
 Try more integration points or a different set of  integration origins.
 Surface Problems in SciFoc.

Does anyone know any solution?

Thanks,

Jorge 


 
   ***********************************************************************  
			MSc. Jorge S.Gancheff
	        
    C醫edra de Qu韒ica Inorg醤ica	 e-mail: jorge@bilbo.edu.uy
    Departamento "Estrella Campos"       Tel.: +598 2 924 9739	
    Facultad de Qu韒ica, UDELAR          Fax:  +598 2 924 1906
    Montevideo, 11800			 URUGUAY	
   *********************************************************************** 



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To: <chemistry@ccl.net>
Subject: XMGRACE; exact diagnosis
Date: Tue, 11 Dec 2001 18:59:46 +0100
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Forgot to say  what was exaclty wrong:
=20
=93 Can=92t initialize GUI , exiting..=93
=20
Is what I get when I run the *bat file.
=20
=20
Cheers
=20
Sergio

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<body lang=3DNO-BOK link=3Dblue vlink=3Dpurple =
style=3D'tab-interval:35.4pt'>

<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Forgot to <span =
class=3DGramE>say<span
style=3D'mso-spacerun:yes'>=A0 </span>what</span> was <span =
class=3DSpellE>exaclty</span>
wrong:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span lang=3DEN-GB
style=3D'font-size:10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>=93 =
Can=92t</span></font></span><font
size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:10.0pt;font-family:Arial;
mso-ansi-language:EN-GB'> initialize GUI , =
exiting..=93<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Is what I get when I =
run the
*bat file.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Cheers<o:p></o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Sergio<o:p></o:p></span=
></font></p>

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From chemistry-request@server.ccl.net Tue Dec 11 12:55:54 2001
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From: "Sergio Manzetti" <sergio@proinformatix.com>
To: <chemistry@ccl.net>
Subject: XMGRACE for Windows
Date: Tue, 11 Dec 2001 18:44:46 +0100
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Dear CCLers thank you all for the link to GRACE homepage, a new problem
has though arised, installing and running the bat file is less easy than
I thought, the discussion topics and FAQs at the GRACE homepage are not
much of help. Maybe someone that uses GRACE for windows (vers. 5.1.5)
could send me their *bat file, or maybe the entire package zipped?
 
 
Best regards
 
Sergio

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<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Dear <span =
class=3DSpellE>CCLers</span>
thank you all for the link to GRACE <span class=3DGramE>homepage</span>, =
a new
problem has though <span class=3DSpellE>arised</span>, installing and =
running the
bat file is less easy than I thought, the discussion topics and <span
class=3DSpellE>FAQs</span> at the GRACE homepage are not much of help. =
Maybe
someone that uses GRACE for windows (<span class=3DSpellE>vers</span>. =
5.1.5)
could send me their *bat file, or maybe the entire package =
zipped?<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'>Best =
regards<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
10.0pt;font-family:Arial;mso-ansi-language:EN-GB'><o:p>&nbsp;</o:p></span=
></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-GB =
style=3D'font-size:
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From chemistry-request@server.ccl.net Tue Dec 11 18:41:22 2001
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Date: Tue, 11 Dec 2001 16:19:08 -0700
To: CHEMISTRY@ccl.net
From: Demetrio Antonio da Silva Filho <dasf@u.arizona.edu>
Subject: CI-Singles - Wrong Excited State Energies?
Mime-Version: 1.0
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Dear CCL'ers,

I am using CI-Singles (in gaussian'98) to optimize the geometry of the first
singlet and triplet excited state.

After getting the energies of those states, I subtracted those numbers from the
ground state energy and then compared with the excited state energies obtained
by running a CI-S calculation  using the ground state geometry.

To my surprise, I found that the first excited state energy, obtained using 
the ground
state geometry, is SMALLER than the energy difference between the first 
excited state
and the ground state energies.

It means that when I optimize the geometry of the excited state using 
CI-Singles, I arrive
at a geometry which energy is HIGHER than the one obtained using the ground 
state geometry
-- the one that I used to begin the CI-S calculation.

Does anybody have any idea of why I get these strange results? Those 
results mean that CI-Singles is not a reliable methodology to optimize 
excited state geometries?

Thanks in advance,

Demetrio Filho


From chemistry-request@server.ccl.net Tue Dec 11 19:41:42 2001
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Date: Tue, 11 Dec 2001 16:41:26 -0800 (PST)
From: PRADIPTA Bandyopadhyay <pradipta@cgl.ucsf.edu>
To: chemistry@ccl.net
Subject: LAPACK!
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 Hi,

   Sorry to bother with a simple yet technical question.

 I am trying to use the 'DGESV' driver routine from LAPACK - this routine
 solves the A * X = B linear equation. However, I am having a problem with
 the array dimension when I call it from my code.

 The arguments of DGESV are DGESV(N,NRHS,A,LDA,IPIV,B,LDB,INFO)

 N= order of the matrix A

 NRHS=column of B

 LDA = leading dimension of A

 IPIV= OUTPUT of dimension N

 LDB= leading dimension of B

 B= N by NHRS


 For a test case: A is 3 *3 , B and X are 3*1.

 N=3, NRHS=1, LDA=3, LDB=3

 
 I think I am giving the correct arguments. Is there any trick/ or am I
 making some silly mistake?
 
 I would appreciate if someone points out my mistake.

                                              Pradipta
 


From chemistry-request@server.ccl.net Tue Dec 11 17:52:50 2001
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From: "Phil Hultin" <hultin@cc.UManitoba.CA>
To: "Computational Chemistry List" <chemistry@ccl.net>
Subject: Re: Gaussian Flame-wars
Date: Tue, 11 Dec 2001 16:52:36 -0600
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Max Valdez wrote:

>I think Gaussian is a great tool, but it has a LOT of little secrets and
>"bugs", and the support is not so good, I don't think the spend that much
money
>on customer support, given the price of the product.

I absolutely agree with this statement.  I think I represent a new kind of
scientist working with tools like Gaussian.  I am an experimentalist, not a
computer whiz, but now that I can get serious computer power for a
reasonable dollar, I want to use serious computational tools to answer
nagging questions about organic chemistry.

Gaussian can do WONDERFUL things, BUT its creators evidently expect that
users are just as computer-savvy and UNIX-proficient as they are.  I have
wasted hours debugging failed jobs, where apparently everything was exactly
as the "User's Reference" said it should be!  For instance, nowhere is it
stated that individual lines in the Route section must be 80 characters or
less - but there it is.  Now, if I had been a little bit older and
remembered that back in the stone age Fortran punch cards had only 80
columns, perhaps I would have twigged to this one sooner.  I could go on and
on...

So what's the point of all this?  Well, maybe people would be less prone to
jump on Gaussian (as they have over this makefile thing) if they didn't feel
that the philosophy of Gaussian Inc. was similar to that of the "high
priest" - only the initiates will have the secrets revealed and then only
after years of study.  A nice start would be to make the program work the
way the manual implies that it should (or to make the manual describe how
the program actually works).  Even better: bring the program into the 21st
century by providing a user interface that is actually user-friendly.  What
the priests and initiates regard as "a philosophy and aesthetic of
simplicity" looks quite otherwise to many of us on the outside!

Dr. Philip G. Hultin
Associate Department Head and
Associate Professor of Chemistry
University of Manitoba
Winnipeg, MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin@cc.umanitoba.ca
http://www.umanitoba.ca/chemistry/