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Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance (fwd from landman_at_scalableinformatics.com)
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----- Forwarded message from Joe Landman <landman_at_scalableinformatics.com> =
-----

From: Joe Landman <landman_at_scalableinformatics.com>
Date: Fri, 21 May 2004 21:30:43 -0400
To: Konstantin Kudin <konstantin_kudin_at_yahoo.com>
Cc: beowulf_at_beowulf.org
Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance
X-Mailer: Ximian Evolution 1.4.4=20

On Fri, 2004-05-21 at 17:23, Konstantin Kudin wrote:
> > Again...SPEC was included, among a number of others. Would you happen
>=20
> > to have a cross section of code relevant to computational chemistry =20
>=20
> > that might offer a fair example of platform performance? I'd enjoy a=20
> > chance to get it into the labs and see how Itanuim 2 might stack up.
>=20
>  While I can't speak for every code out there, for Gaussian03 I2 seems
> to work extremely well:
> http://www.princeton.edu/~kkudin/g03_b5_tests_1.txt

Looks interesting.  From the text, "All Intel compatible hardware ran
under RedHat 9.0, in 32 bits."  I presume you ran the I2 as a 64 bit OS
using pgf77?  or g77/ifc?  Also you used the Atlas libs for p4.  Same
ones for O16 and O20?

I would be curious to see the performance with a 64 bit compilation
running under a 64 bit OS (SuSE 9.x)

>  Note that these are ~1 hour long jobs, which surely do not fit in
> cache.

Well, length of time doesn't indicate cache fit.  Gaussian (depending
upon the module) will significantly overflow cache, and sometimes main
memory.  Disk I/O bandwidth and organization matter for performance on
the larger analysis, though anything spilling to disk is going to be
slow.

>  The interesting part is that for some real life codes I2 performance
> matches what SPEC numbers would predict. The cost, of course, is a
> different issue altogether.

The I2 is an interesting beast.  Then again, so is the Opteron, and the
G5.


--=20
Joe Landman <landman_at_scalableinformatics.com>

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From chemistry-request@ccl.net Mon May 24 02:11:21 2004
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Date: Mon, 24 May 2004 03:13:02 -0400
From: Kadir Diri <kadir/at/visual1.chem.pitt.edu>
Subject: freezing atoms in frequency calculations
To: chemistry/at/ccl.net
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Dear all,
I wonder if there is an ab initio code that lets one freeze all atoms 
but one in a large molecule, and calculate the frequency related to the 
atom which was not not frozen, say, like calculating the frequency of a 
single OH stretch in some molecule?
Thank you in advance!
kadir




From chemistry-request@ccl.net Mon May 24 06:03:22 2004
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From: "Muneerah" <mmogren!at!ksu.edu.sa>
To: <CHEMISTRY!at!ccl.net>
Subject: program for normal coordinate
Date: Mon, 24 May 2004 14:05:33 +0300
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Dear all

Does anyone has suggestions of a good program for normal coordinate
analysis which would work on a pc and if possible, since I am working on
a large molecule, would generate the internal coordinates.

Best regards,

M. Mogren

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<DIV>Dear all<BR><BR>Does anyone has suggestions of a good program for =
normal=20
coordinate<BR>analysis which would work on a pc and if possible, since I =
am=20
working on<BR>a large molecule, would generate the internal=20
coordinates.<BR><BR>Best regards,<BR><BR>M. =
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From chemistry-request@ccl.net Mon May 24 06:01:27 2004
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From: "humayun kabir" <kabir50!at!hotmail.com>
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Subject: DFT:optimization trouble
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<DIV>
<P><FONT face="Times New Roman, Times, Serif" size=3>Dear CCL scientist,</FONT></P>
<P><FONT face="Times New Roman, Times, Serif" size=3>I have some difficullty in optimizing an aromatic &nbsp;molecule in DFT method. I used the following steps in order to optimize the molecule at a medium basis (6-31g*) set in DFT. For that I started from a low level optimizatization which I subsequently used for the next step.<BR></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>1. First I optimized&nbsp;the molecule&nbsp;at hf/3-21g* level.<BR><BR>2. Then at b3lyp/3-21g* level (<STRONG>route section:</STRONG> # opt b3lpy/3-21g* geom=check<BR>guess=read).<BR><BR>3.&nbsp;Then I tried at&nbsp;</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>b3lyp/6-31g*level (<STRONG>route section:</STRONG> # opt b3lpy/6-31g*<BR>geom=check guess=read).</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><STRONG>&nbsp;In this step gaussian terminated with an error message ( Number of steps exceeded NStep= 154).</STRONG></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman">&nbsp;<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>4.&nbsp; I also tried at </FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>b3lyp/6-31g*level&nbsp; </FONT><FONT face="Times New Roman" size=3># opt=(Tight,MaxCycle=200, MaxStep=200) </FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp; </SPAN>Item<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>Value<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>Threshold<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </SPAN>Converged?</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN>Maximum Force<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.000087<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.000015<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>NO </FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN>RMS<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>Force<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.000025<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.000010<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>NO </FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN>Maximum Displacement<SPAN style="mso-spacerun: yes">&nbsp; </SPAN>0.064004<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.000060<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>NO </FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN>RMS<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>Displacement<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.015132<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>0.000040<SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>NO </FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN>Predicted change in Energy=-2.691597D-04</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN>Optimization stopped.</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </SPAN><B><SPAN style="COLOR: red">-- Number of steps exceeded,<SPAN style="mso-spacerun: yes">&nbsp; </SPAN>NStep= 180<o:p></o:p></SPAN></B></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </SPAN>-- Flag reset to prevent archiving.</FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3></FONT>&nbsp;</P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>I cannot understand where is the problem. Would you please give me&nbsp;some suggestions/hints concerning my problem. Thank you all for your time and kind cooperation.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3></FONT>&nbsp;</P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>With best wishes, KABIR</FONT></P><BR><BR>
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From chemistry-request@ccl.net Sun May 23 20:26:46 2004
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References: <20040202235310.20e965e2.a_sutcliffe!at!iprimus.com.au> <opr8fnpbjnkdab1u!at!mail.telepac.pt>
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Cc: "Alex Sutcliffe" <a_sutcliffe!at!iprimus.com.au>, chemistry!at!ccl.net
From: Kim Branson <kim.branson!at!csiro.au>
Subject: Re: CCL:using DOCK without sybil
Date: Mon, 24 May 2004 11:29:38 +1000
To: "Filipe Maia" <fmaia!at!gmx.net>
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Hi,

there are some tools at
http://home.pchome.com.tw/team/gentamicin/mol/mol.htm

which will take a pdb file, add protons and kollman charges and write  
out a mol2 file for you. You may need to minimise the final proton  
positions with another tool.

cheers


Kim


On 23/05/2004, at 1:23 PM, Filipe Maia wrote:

> On Mon, 2 Feb 2004 23:53:10 +1100, Alex Sutcliffe  
> <a_sutcliffe!at!iprimus.com.au> wrote:
>
>> Hi CCLers,
>>
>> I would like to use DOCK but don't have access to sybil. In order to  
>> convert my molecules to mol2 format I had hoped to use openbabel to  
>> do a simple conversion, however GRID gave me this:
>>
>> Improper ATOM record substructure id for ***** in ./mymolecule.mol2
>
> http://home.pchome.com.tw/team/gentamicin/mol/mol.htm
> I don't know if pmol2q is of any help.
>
>>
>> I do have an example of a molecule in mol2 format that is acceptable  
>> which I intend to compare with mymolecule with but I just thought  
>> that someone else had probably been down this road already.
>>
>> Any much appreciated!
>>
>> Alex Sutcliffe
>>
>>
>>
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From chemistry-request@ccl.net Mon May 24 04:07:53 2004
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Subject: Keto-enol tautomerism studies
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Dear CCLers,

	I'm looking for some general references about keto-enol tautomerism studies with different semiempirical and/or ab initio methods (... not sure about goodness of my keywords in article retrieval). I'm particularly interested in methods comparison.

I'll summarize all replies.

Best regards,

Roberto Forlani



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From: Mathias Weigt <m.weigt^at^uni-bonn.de>
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To: CHEMISTRY^at^ccl.net
Subject: Re: CCL:DFT:optimization trouble
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On Monday 24 May 2004 13:04, humayun kabir wrote:
> <html><div style='background-color:'><DIV>
... not readable
please use plain-text

-- 
Mathias Weigt

From chemistry-request@ccl.net Mon May 24 12:18:41 2004
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From: Daniel Singleton <singleton)at(mail.chem.tamu.edu>
Subject: CCL: Re: DFT:optimization trouble
Date: Mon, 24 May 2004 12:20:11 -0500
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Take your latest geometry and resubmit using # b3lyp/6-31G* =20
opt=3D(tight,calcfc)
That should solve the problem most of the time, but read up about the =20=

gaussian keyword "opt" on their web site to learn about other options =20=

to get initial force constants, such as "calcall".

On May 24, 2004, at 6:04 AM, humayun kabir wrote:

> Dear CCL scientist,
>
> I have some difficullty in optimizing an aromatic =A0molecule in DFT =20=

> method. I used the following steps in order to optimize the molecule =20=

> at a medium basis (6-31g*) set in DFT. For that I started from a low =20=

> level optimizatization which I subsequently used for the next step.
>
> 1. First I optimized=A0the molecule=A0at hf/3-21g* level.
>
> 2. Then at b3lyp/3-21g* level (route section: # opt b3lpy/3-21g* =20
> geom=3Dcheck
> guess=3Dread).
>
> 3.=A0Then I tried at=A0
>
> b3lyp/6-31g*level (route section: # opt b3lpy/6-31g*
> geom=3Dcheck guess=3Dread).
>
> =A0In this step gaussian terminated with an error message ( Number of =20=

> steps exceeded NStep=3D 154).
>
> =A0
>
> 4.=A0 I also tried at
>
>  b3lyp/6-31g*level=A0 # opt=3D(Tight,MaxCycle=3D200, MaxStep=3D200)
>
>  =A0 Item=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Value=A0=A0=A0=A0=A0=A0=A0=A0=A0 =
Threshold=A0=A0=A0 =20
> Converged?
>
> =A0Maximum Force=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =
0.000087=A0=A0=A0=A0 0.000015=A0=A0=A0=A0=A0=A0 NO
>
>  =A0RMS=A0=A0=A0=A0 Force=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 0.000025=A0=A0=A0=A0 0.000010=A0=A0=A0=A0=A0=A0 NO
>
>  =A0Maximum Displacement=A0 0.064004=A0=A0=A0=A0 0.000060=A0=A0=A0=A0=A0=
=A0 NO
>
>  =A0RMS=A0=A0=A0=A0 Displacement=A0=A0=A0=A0=A0 0.015132=A0=A0=A0=A0 =
0.000040=A0=A0=A0=A0=A0=A0 NO
>
>  =A0Predicted change in Energy=3D-2.691597D-04
>
> =A0Optimization stopped.
>
> =A0=A0=A0 -- Number of steps exceeded,=A0 NStep=3D 180
>
> =A0=A0=A0 -- Flag reset to prevent archiving.
>
> =A0
>
> I cannot understand where is the problem. Would you please give =20
> me=A0some suggestions/hints concerning my problem. Thank you all for =20=

> your time and kind cooperation.
>
> =A0
>
> With best wishes, KABIR
>
>
>
>
>
> MSN 8 helps ELIMINATE E-MAIL VIRUSES. Get 2 months FREE*.
> -=3D This is automatically added to each message by the mailing script =
=3D-
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> +-+
>
>
>

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Take your latest geometry and resubmit using # b3lyp/6-31G*
opt=3D(tight,calcfc)

That should solve the problem most of the time, but read up about the
gaussian keyword "opt" on their web site to learn about other options
to get initial force constants, such as "calcall".


On May 24, 2004, at 6:04 AM, humayun kabir wrote:


<excerpt><fontfamily><param>Times New Roman</param>Dear CCL =
scientist,</fontfamily>


<fontfamily><param>Times New Roman</param>I have some difficullty in
optimizing an aromatic =A0molecule in DFT method. I used the following
steps in order to optimize the molecule at a medium basis (6-31g*) set
in DFT. For that I started from a low level optimizatization which I
subsequently used for the next step.</fontfamily>


<fontfamily><param>Times New Roman</param>1. First I optimized=A0the
molecule=A0at hf/3-21g* level.</fontfamily>


<fontfamily><param>Times New Roman</param>2. Then at b3lyp/3-21g*
level (<bold>route section:</bold> # opt b3lpy/3-21g* =
geom=3Dcheck</fontfamily>

<fontfamily><param>Times New Roman</param>guess=3Dread).</fontfamily>


<fontfamily><param>Times New Roman</param>3.=A0Then I tried =
at=A0</fontfamily>


<fontfamily><param>Times New Roman</param>b3lyp/6-31g*level
(<bold>route section:</bold> # opt b3lpy/6-31g*</fontfamily>

<fontfamily><param>Times New Roman</param>geom=3Dcheck =
guess=3Dread).</fontfamily>


<bold><fontfamily><param>Times New Roman</param>=A0In this step gaussian
terminated with an error message ( Number of steps exceeded NStep=3D
154).</fontfamily></bold>


<fontfamily><param>Times New Roman</param>=A0</fontfamily>


<fontfamily><param>Times New Roman</param>4.=A0 I also tried =
at</fontfamily>


<fontfamily><param>Times New Roman</param> b3lyp/6-31g*level=A0 #
opt=3D(Tight,MaxCycle=3D200, MaxStep=3D200)</fontfamily>


<fontfamily><param>Times New Roman</param> =A0
Item=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0 Value=A0=A0=A0=A0=A0=A0=A0=A0=A0 Threshold=A0=A0=A0
Converged?</fontfamily>


<fontfamily><param>Times New Roman</param>=A0Maximum Force=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0
0.000087=A0=A0=A0=A0 0.000015=A0=A0=A0=A0=A0=A0 NO</fontfamily>


<fontfamily><param>Times New Roman</param> =A0RMS=A0=A0=A0=A0
Force=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000025=A0=A0=
=A0=A0 0.000010=A0=A0=A0=A0=A0=A0 NO</fontfamily>


<fontfamily><param>Times New Roman</param> =A0Maximum Displacement=A0
0.064004=A0=A0=A0=A0 0.000060=A0=A0=A0=A0=A0=A0 NO</fontfamily>


<fontfamily><param>Times New Roman</param> =A0RMS=A0=A0=A0=A0 =
Displacement=A0=A0=A0=A0=A0
0.015132=A0=A0=A0=A0 0.000040=A0=A0=A0=A0=A0=A0 NO</fontfamily>


<fontfamily><param>Times New Roman</param> =A0Predicted change in
Energy=3D-2.691597D-04</fontfamily>


<fontfamily><param>Times New Roman</param>=A0Optimization =
stopped.</fontfamily>


<fontfamily><param>Times New Roman</param>=A0=A0=A0
<bold><color><param>FFFF,0000,0000</param>-- Number of steps
exceeded,=A0 NStep=3D 180</color></bold></fontfamily>


<fontfamily><param>Times New Roman</param>=A0=A0=A0 -- Flag reset to =
prevent
archiving.</fontfamily>


=A0


<fontfamily><param>Times New Roman</param>I cannot understand where is
the problem. Would you please give me=A0some suggestions/hints
concerning my problem. Thank you all for your time and kind
cooperation.</fontfamily>


=A0


<fontfamily><param>Times New Roman</param>With best wishes, =
KABIR</fontfamily>






MSN 8 helps <color><param>0000,0000,EEEE</param>ELIMINATE E-MAIL
VIRUSES.</color> Get 2 months FREE*.=20

<fixed>-=3D This is automatically added to each message by the mailing
script =3D-

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</fixed>

</excerpt>=

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From chemistry-request@ccl.net Mon May 24 12:53:27 2004
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From: "Dr. Daniel Glossman-Mitnik" <daniel.glossman..at..cimav.edu.mx>
To: <CHEMISTRY..at..ccl.net>, <help..at..gaussian.com>
Subject: CCL: more questions about ONIOM in G03W
Date: Mon, 24 May 2004 11:56:19 -0600
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=20

Hi !!!

=20

Thanks for your answers to my previous questions about ONIOM in=20

G03W. I have a couple of additional questions:

=20

1) when I calculate NMR, I use to include in the route IOP(10/6=3D1) in

     order to calculate the magnetizability. In a standard calculation =
the

     results and the units are clear, but I am not sure about the =
results

     in ONIOM.  Could you clarify this ?

=20

2) In a standard calculation I use GaussViewW to recover the .chk

     file, and in this way to plot the total density or the molecular

     orbitals. Nevertheless, I have not be able to do the same thing

     with the results of an ONIOM calculation. Is there any way to

     do the trick (may be some keyword or IOP) ?

=20

3) I said two, but I have one more. I use to define my functional

    using  and IOP (i.e.   pbepbe/6-31G*  IOp(3/76=3D0500005000)).

    Can be this IOp be carried through different steps ?

    I want to calculate hyperpolarizabilities and I know that this must

    be done within DFT using Polar=3DEnonly. This implies a numerical

    procedure. Can my definition of functional (with an Iop) be used

    to calculate numerical hyperpolarizabilites ?

=20

4) And, of course, one more. I have been reading the manuals about

     how to create an input for a PBC calculation. I think I have =
understood

     it, but not totally. Thus, I have certain doubts. Can you send me =
an

     input example for polythiophene, so I check it and be able to =
create

     my own polymers ?

=20

Thanks in advance.  Best regards

=20

                                             Dr. Daniel Glossman-Mitnik=20

=20

=20

*************************************************************************=
***
**********************

            Dr. Daniel Glossman-Mitnik

=20

CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC=20

QCOSMO - Grupo de Qu=EDmica Computacional, Simulaci=F3n y Modelado =
Molecular

Miguel de Cervantes 120 - Complejo Industrial Chihuahua

Chihuahua, Chih. 31109 - MEXICO

Tel=E9fono: (52) 614 4391151                FAX:       (52) 614 4391112

E-mail:    daniel.glossman..at..cimav.edu.mx    dglossman..at..prodigy.net.mx =20

P=E1gina WEB:  http://www.cimav.edu.mx       http://www.qcosmo.org=20

*************************************************************************=
***
***********************

=20

=20


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<div class=3DSection1>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
style=3D'font-size:
12.0pt;font-family:Arial;color:black'>Hi !!!</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
style=3D'font-size:
12.0pt;font-family:Arial;color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>Thanks for your =
answers
to my previous questions about ONIOM in </span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>G03W. I have a =
couple of
additional questions:</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal style=3D'text-indent:-18.0pt'><font size=3D3 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:12.0pt;font-family:Arial;
color:black'>1) when I calculate NMR, I use to include in the route =
IOP(10/6=3D1)
in</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;
&nbsp;&nbsp;order to calculate the magnetizability. In a standard =
calculation
the</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
results and the units are clear, but I am not sure about the =
results</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
in ONIOM.&nbsp; Could you clarify this ?</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal style=3D'text-indent:-18.0pt'><font size=3D3 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:12.0pt;font-family:Arial;
color:black'>2) In a standard calculation I use GaussViewW to recover =
the .chk</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;
&nbsp;file, and in this way to plot the total density or the =
molecular</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
orbitals. Nevertheless, I have not be able to do the same =
thing</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
with the results of an ONIOM calculation. Is there any way =
to</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
do the trick (may be some keyword or IOP) ?</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal style=3D'text-indent:-18.0pt'><font size=3D3 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:12.0pt;font-family:Arial;
color:black'>3) I said two, but I have one more. I use to define my =
functional</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;
&nbsp;using&nbsp; and IOP (i.e.&nbsp;&nbsp; pbepbe/6-31G*&nbsp;
IOp(3/76=3D0500005000)).</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p; Can
be this IOp be carried through different steps ?</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p; I
want to calculate hyperpolarizabilities and I know that this =
must</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p; be
done within DFT using Polar=3DEnonly. This implies a =
numerical</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;
procedure. Can my definition of functional (with an Iop) be =
used</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p; to
calculate numerical hyperpolarizabilites ?</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal style=3D'text-indent:-18.0pt'><font size=3D3 =
color=3Dblack
face=3DArial><span lang=3DEN-US =
style=3D'font-size:12.0pt;font-family:Arial;
color:black'>4) And, of course, one more. I have been reading the =
manuals about</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
how to create an input for a PBC calculation. I think I have =
understood</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
it, but not totally. Thus, I have certain doubts. Can you send me =
an</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
input example for polythiophene, so I check it and be able to =
create</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbs=
p;&nbsp;
my own polymers ?</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>Thanks in =
advance.&nbsp;
Best regards</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
lang=3DEN-US
style=3D'font-size:12.0pt;font-family:Arial;color:black'>&nbsp;</span></f=
ont></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
style=3D'font-size:
12.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;
Dr. Daniel Glossman-Mitnik </span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>***********************************=
***************************************************************</span></f=
ont></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>&nbsp;&nbsp;&nbsp;&nbsp;<img =
width=3D166
height=3D116 src=3D"cid:image002.gif@01C44186.1E753F40" =
border=3D0>&nbsp;&nbsp;&nbsp;
&nbsp;&nbsp;&nbsp; </span></font><font size=3D4 color=3Dblack =
face=3DArial><span
style=3D'font-size:13.5pt;font-family:Arial;color:black'>Dr. Daniel
Glossman-Mitnik</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:black'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3DArial><span =
style=3D'font-size:
12.0pt;font-family:Arial;color:black'>CIMAV</span></font><font size=3D2
color=3Dblack face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'> - Centro de Investigaci=F3n en Materiales Avanzados, SC =
</span></font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Minya =
Nouvelle"><span
style=3D'font-size:12.0pt;font-family:"Minya =
Nouvelle";color:black'>QCOSMO</span></font><font
size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
color:black'> - Grupo de Qu=EDmica Computacional, Simulaci=F3n y =
Modelado Molecular</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Miguel de Cervantes 120 - Complejo
Industrial Chihuahua</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Chihuahua, Chih. 31109 - =
MEXICO</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>Tel=E9fono: (52) 614
4391151&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;
FAX:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (52) 614 =
4391112</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>E-mail:&nbsp;&nbsp;&nbsp; <a
href=3D"mailto:daniel.glossman..at..cimav.edu.mx">daniel.glossman..at..cimav.edu.mx=
</a>&nbsp;&nbsp;&nbsp;
<a =
href=3D"mailto:dglossman..at..prodigy.net.mx">dglossman..at..prodigy.net.mx</a>&nbs=
p; </span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>P=E1gina WEB:&nbsp; <a
href=3D"http://www.cimav.edu.mx">http://www.cimav.edu.mx</a>&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;
<a href=3D"http://www.qcosmo.org">http://www.qcosmo.org</a> =
</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:black'>***********************************=
****************************************************************</span></=
font></p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:black'>&nbsp;</span></font></p>

<p style=3D'margin-left:1063.5pt'><font size=3D2 color=3D"#0033cc" =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial;color:#0033CC'>&nbsp;</span><=
/font></p>

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From chemistry-request@ccl.net Mon May 24 13:06:16 2004
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	Mon, 24 May 2004 20:09:07 +0200 (METDST)
Date: Mon, 24 May 2004 20:09:07 +0200 (METDST)
From: Frank Jensen <frj<<at>>dou.dk>
To: Eugen Leitl <eugen<<at>>leitl.org>
cc: chemistry<<at>>ccl.net
Subject: Re: CCL:[Beowulf] Question regarding Mac G5 performance (fwd from
 landman<<at>>scalableinformatics.com)
In-Reply-To: <20040524112909.GP1105<<at>>leitl.org>
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	For those interested in the performance of
electronic structure methods on various cpu's, you may want
to check out some data we have compiled:
http://www.dcsc.sdu.dk/Benchmarks.html
The Itanium-2 is probably the fastest cpu for these
types of calculations, the Opteron is interesting
for 64-bit applications due to the lower price tag, 
but for 32-bit applications, a straight Pentium-4
is still hard to beat from a performance/price point of view.
	Frank


On Mon, 24 May 2004, Eugen Leitl wrote:

> ----- Forwarded message from Joe Landman <landman<<at>>scalableinformatics.com> -----
> 
> From: Joe Landman <landman<<at>>scalableinformatics.com>
> Date: Fri, 21 May 2004 21:30:43 -0400
> To: Konstantin Kudin <konstantin_kudin<<at>>yahoo.com>
> Cc: beowulf<<at>>beowulf.org
> Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance
> X-Mailer: Ximian Evolution 1.4.4 
> 
> On Fri, 2004-05-21 at 17:23, Konstantin Kudin wrote:
> > > Again...SPEC was included, among a number of others. Would you happen
> > 
> > > to have a cross section of code relevant to computational chemistry  
> > 
> > > that might offer a fair example of platform performance? I'd enjoy a 
> > > chance to get it into the labs and see how Itanuim 2 might stack up.
> > 
> >  While I can't speak for every code out there, for Gaussian03 I2 seems
> > to work extremely well:
> > http://www.princeton.edu/~kkudin/g03_b5_tests_1.txt
> 
> Looks interesting.  From the text, "All Intel compatible hardware ran
> under RedHat 9.0, in 32 bits."  I presume you ran the I2 as a 64 bit OS
> using pgf77?  or g77/ifc?  Also you used the Atlas libs for p4.  Same
> ones for O16 and O20?
> 
> I would be curious to see the performance with a 64 bit compilation
> running under a 64 bit OS (SuSE 9.x)
> 
> >  Note that these are ~1 hour long jobs, which surely do not fit in
> > cache.
> 
> Well, length of time doesn't indicate cache fit.  Gaussian (depending
> upon the module) will significantly overflow cache, and sometimes main
> memory.  Disk I/O bandwidth and organization matter for performance on
> the larger analysis, though anything spilling to disk is going to be
> slow.
> 
> >  The interesting part is that for some real life codes I2 performance
> > matches what SPEC numbers would predict. The cost, of course, is a
> > different issue altogether.
> 
> The I2 is an interesting beast.  Then again, so is the Opteron, and the
> G5.
> 
> 
> -- 
> Joe Landman <landman<<at>>scalableinformatics.com>
> 
> _______________________________________________
> Beowulf mailing list, Beowulf<<at>>beowulf.org
> To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
> 
> ----- End forwarded message -----
> -- 
> Eugen* Leitl <a href="http://leitl.org">leitl</a>
> ______________________________________________________________
> ICBM: 48.07078, 11.61144            http://www.leitl.org
> 8B29F6BE: 099D 78BA 2FD3 B014 B08A  7779 75B0 2443 8B29 F6BE
> http://moleculardevices.org         http://nanomachines.net
> 

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| University of Southern Denmark                 |
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From chemistry-request@ccl.net Mon May 24 11:28:50 2004
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Subject: van der Waal's radius from Universal Force Field (UFF) 
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Dear all,

In Gaussian quantum chemical software, UFF (Universal Force Field)
radii can be choosen for building a cavity of molecule in SCRF
calculation.

Does anybody know how these UFF radii come from, especially the Pt
atom?

For example, the UFF radius for Pt atom is 1.72 in Gaussian 98 SCRF=PCM
calculation. 

Thank you for your attention.

Best regards,

Patrick


From chemistry-request@ccl.net Mon May 24 16:58:27 2004
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From: "Yubo Fan" <yubofan*at*mail.chem.tamu.edu>
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Subject: reference for LANL2DZdp
Date: Mon, 24 May 2004 17:01:14 -0500
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Hi,

I've downloaded LANL2DZdp basis sets for H, C, N and O from EMSL Gaussian
Basis Set Order Form, but I cannot find the references of the d poralization
and p diffuse functions for these elements. The references lised there are
just for LANL2DZ and d, p functions for the third row elements and below.
Could you help me to find out the references for H and the first row p-block
elements. Thanks in advance.

Yubo
============================================================
Dr. Yubo Fan               Email: yubofan*at*mail.chem.tamu.edu
Department of Chemistry    Tel:   1-979-845-7222
Texas A&M University
College Station, TX 77843
============================================================