From chemistry-request@ccl.net Thu May 12 16:04:56 2005
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Reply-To: "Alex. A. Granovsky" <gran !=! classic.chem.msu.su>
From: "Alex. A. Granovsky" <gran !=! classic.chem.msu.su>
To: <khunter !=! mta.ca>, <CHEMISTRY !=! ccl.net>
References: <1115825475.428225438ceff !=! webmail.mta.ca>
Subject: Re: CCL:DE2Siz in DoE2D error
Date: Thu, 12 May 2005 22:36:49 +0400
Organization: MSU
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Dear Ken,

for single-point MP2 energy calculations try to use PC GAMESS.
It has state-of-the-art parallel MP2 implementation with extremely 
low memory demands, which was tested on systems with up to 4000 
basis functions and on clusters of up to 64 nodes. 

Best regards,
Alex Granovsky,
the PC GAMESS project.


----- Original Message ----- 
From: <khunter !=! mta.ca>
To: <CHEMISTRY !=! ccl.net>
Sent: Wednesday, May 11, 2005 7:31 PM
Subject: CCL:DE2Siz in DoE2D error


> The following error arises when attempting to model semi-large systems with 
> MP2 with Gaussian 03 on a Linux cluster.   
> 
> 
> Disk-based method using O(N**2) memory for 10 occupieds at a time.
>  Estimated scratch disk usage=          -1 words.
>  Inconsistency from DE2Siz in DoE2D.
> 
> 
> Changing the memory, disk space, and %rwf appear to have no affect.  Any 
> assisstance on how to correct this error would be greatly appreaciated.
> 
> Ken Hunter
> Mount Allison University
> 
> -= This is automatically added to each message by the mailing script =-
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From chemistry-request@ccl.net Thu May 12 16:36:54 2005
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Date: Thu, 12 May 2005 14:30:53 -0500
From: alterrc/at/charlotte.lfc.edu
Subject: ONIOM frequency Calculation
To: chemistry/at/ccl.net
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I am running a 2-layered ONIOM frequency calculation on Gaussian '03.
The higher level is a b3lyp/lanl2mb and the lower is UFF. After the
engery calculation if finished, the error message "Uncompressed Fx but
compression in L1002." is received and the calculation terminated. Can
anyone help me to understand this error and what I can do to fix it?

Rachel C. Alter

alterrc/at/lfc.edu


From chemistry-request@ccl.net Thu May 12 13:23:21 2005
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Subject: CCL:Keeping coordinates fixed in g03 ONIOM calculation
Date: Thu, 12 May 2005 18:19:26 +0200
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Thread-Topic: CCL:Keeping coordinates fixed in g03 ONIOM calculation
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From: "Crous Werner <wcrous/at/sun.ac.za>" <wcrous/at/sun.ac.za>
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Hello CCL

=20

I have a problem in fixing the Cartesian coordinates in an ONIOM
calculation with g03. I have used opt=3D(Modredundant) and I did give =
the
correct input after the cartesian coordinates, but when I run the
calculation my coordinates are changed in the MM-layer and do not stay
fixed. Is it possible to fix the coordinates in g03? I would really
appreciate any help. Thank you.

=20

Werner=20

=20

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Werner Crous

MSc. student

Department of Chemistry and Polymer Science

University of Stellenbosch

South Africa

Tel. +27  218083779

Cell. +27 824093822

Email:wcrous/at/sun.ac.za

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~=20

=20

=20


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

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

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I have a problem in fixing the Cartesian coordinates =
in an
ONIOM calculation with g03. I have used opt=3D(Modredundant) and I did =
give the
correct input after the cartesian coordinates, but when I run the =
calculation
my coordinates are changed in the MM-layer and do not stay fixed. Is it
possible to fix the coordinates in g03? I would really appreciate any =
help.
Thank you.</span></font></p>

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

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

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

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

<p class=3DMsoNormal><strong><b><font size=3D2 color=3Dnavy =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Werner =
Crous</span></font></b></strong></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>MSc. student</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Department of Chemistry and Polymer
Science</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
  10.0pt;font-family:Arial;color:navy'>University</span></font><font =
size=3D2
 color=3Dnavy face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;
 color:navy'> of </span></font><font size=3D2 color=3Dnavy =
face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Stellenbosch</spa=
n></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>South Africa</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Tel. +27&nbsp; =
218083779</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Cell. +27 =
824093822</span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Email:wcrous/at/sun.ac.za</span></font>=
</p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</=
span></font><font
color=3Dnavy><span style=3D'color:navy'>&nbsp;</span></font></p>

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

</div>

</body>

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From chemistry-request@ccl.net Thu May 12 02:13:17 2005
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From: "Xiaobo, , Zheng" <xiaobo/at/u.arizona.edu>
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Subject: W:Transition state location for heterogeneous reaction in Gaussian
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Dear CCLer,

I have problems locating transition states of heterogeneous reactions. The transition state structures are usually complicated for reactions involving around 20 atoms including the reactant and catalyst cluster. Does anybody have experience locating this type of TS? What could be a good initial gemetry guess? Is Gaussin keyword OPT=QST2 or QST3 useful in this case? 

Thanks in advance and your inputs are greatly appreciated.

Sincerely,

Xiaobo Zheng




From chemistry-request@ccl.net Wed May 11 23:54:35 2005
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Date: Thu, 12 May 2005 11:50:44 +0800 (HKT)
From: lhhu/at/yangtze.hku.hk
To: David Santos Carballal <david/at/fq.uh.cu>
cc: chemistry/at/ccl.net
Subject: Re: CCL:Tinker input file 2
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Dear David,

Thank you very much for your reply. Actually I tried the way you told me 
before. I think the most trouble thing is that I have to assign those 
atomic force field types manually. Is there any automatic way to do 
this? I am wondering if the molecules are really big, how it can be done 
in this way? It is really time consuming.

Best wishes,

Holly

On Wed, 11 May 2005, David Santos Carballal wrote:

> I forgot:
> You would find the pdbxyz.exe in the bin directory of TINKER, if you run
> it from Windows
>
> David Santos Carballal
>
> On Wed, 11 May 2005 lhhu/at/yangtze.hku.hk wrote:
>
>>
>> Dear all CCLers,
>>
>> I would like to use free TINKER to calculated molecular dynamics. But the
>> input file of tinker seems difficult to generate because the int or xyz
>> file need to be assigned force field atom type first. Can anyone tell me
>> about the most convenient way to generate the input xyz or int file? Is
>> there any free program I can use?
>>
>> Thank you very much,
>>
>> Holly
>>
>>
>> -= This is automatically added to each message by the mailing script =-
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>>
>



From chemistry-request@ccl.net Thu May 12 06:55:32 2005
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Subject: Orientation of orbitals
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Dear Colleagues:
 
I want to ask a question on orbitals obtained from Gaussion calculations. But I am not sure whether I framed my question properly or not.

I want to know the quantitative details of the orbitals obtained from Gaussian calculations. I use Molden software to view the orbitals (but, I am not very familiar with this). But I am interested in the "3D contour" map so that, we can view the concentration of the electrons. By this way, I want to see the extent by which the electrons sticks out in z-direction. 
 
Is this possible to do using Molden? If not, is there any other software (free) by which I can view the orbitals/orientation of the orbitals.
 
Thanks in advance,
 
Sincerely,
Mahesh




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<DIV>Dear Colleagues:</DIV>
<DIV>&nbsp;</DIV>
<DIV>I want to ask a question on orbitals obtained from Gaussion calculations. But I am not sure whether&nbsp;I framed&nbsp;my&nbsp;question&nbsp;properly or not.<BR><BR>I want to know the quantitative details of the orbitals obtained from Gaussian calculations.&nbsp;I use Molden software to view the orbitals (but, I am not very familiar with this). But I am interested in the "3D <EM>contour</EM>" map so that, we can view the concentration of the electrons. By this way, I want to see the extent by which the electrons sticks out in z-direction. </DIV>
<DIV>&nbsp;</DIV>
<DIV>Is this possible to do using Molden? If not, is there any other software (free) by which I can view the orbitals/orientation of the orbitals.</DIV>
<DIV>&nbsp;</DIV>
<DIV>Thanks in advance,</DIV>
<DIV>&nbsp;</DIV>
<DIV>Sincerely,</DIV>
<DIV>Mahesh<BR><BR><BR></DIV><p>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam?  Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com 
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From chemistry-request@ccl.net Thu May 12 02:48:14 2005
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----- Forwarded message from Mikhail Kuzminsky <kus|at|free.net> -----

From: Mikhail Kuzminsky <kus|at|free.net>
Date: Wed, 11 May 2005 22:26:04 +0400
To: Eugen Leitl <eugen|at|leitl.org>
Cc: beowulf|at|beowulf.org
Subject: Re: [Beowulf] CCL:Opteron or Nocona ? (fwd from
	m.somers|at|chem.leidenuniv.nl)
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In message from Eugen Leitl <eugen|at|leitl.org> (Mon, 9 May 2005 
23:24:11 +0200):
>----- Forwarded message from mark somers 
><m.somers|at|chem.leidenuniv.nl> -----
>
>From: mark somers <m.somers|at|chem.leidenuniv.nl>
>Date: Mon, 9 May 2005 09:38:06 +0200
>To: Luigi Cavallo <cavallo|at|chemistry.unina.it>
>Cc: chemistry|at|ccl.net
>Subject: CCL:Opteron or Nocona ?
>User-Agent: KMail/1.6.2
>
>Dear Luigi Cavallo,
>
>we have recently purchased and setup a new Beowulf cluster here in 
>Leiden, 
>dedicated to run ADF and other DFT codes (Dacapo and Vasp) on it. We 
>have 
>found the Nocona's, in combination with the Intel compilers, to be 
>the best 
>combination especially for ADF and ADF-BAND.
>
>Before we decided to go for the Nocona's, we did try with two test 
>machines, 
>one being a dual-cpu AMD Opteron 246 (2.0 GHz) and the other being a 
>dual-cpu 
>Nocona (3.0 GHz). Tests showed that the AMD has, in general, a 
>slightly 
>better cache hierarchy and a better memory scalability, but also that 
>the 
>lack of compilers able to tune for the Opterons is severe. Of course 
>we took 
>the differences in cpu clocks into account.
>
>As it turns out, after having contacted the SCM people in Amsterdam, 
>ADF can 
>effectively use the SSE3 registers and cpu intruction set and that 
>makes it 
>run fast on the Nocona's. This, together with the prices being 
>roughly the 
>same, made us decide to go for the Nocona's. 
>
>BTW, maybe this is known to you already, but Intel offers you their 
>OpenMP 
>capable compilers for free for academic use.

Sorry for big delay w/answer: today is 1st working day after May's 
holidays here in Russia ;-)

I've no doubts that in average Opteron is today better, in particular 
for computational chemistry codes. The reasons is both performance 
(for
"top frequency" chips) and price/performance ratio. We stop to use 
Intel x86 for computational chemistry and began to use AMD from 
"Athlon
times" - because of price/performance reason. But now Opteron is in
average absolutely better due to

a) single CPU performance (See, for example, SPECfp2000 which includes 
also some molecular dynamics codes)
b) power dissipation (which is lower for AMD)
c) dual (and higher also:-)) CPU system architecture: 2 Opteron's
have 2 independed pathes to main memory instead of common system bus
in the case of Nocona. As a result, Opteron's have much more good 
memory throughput scalability. 

Pls take into account that many modern quantum chemistry codes (like 
G03) are "restricted" by memory throughput !

What is about compilers, it was answered in a set of previous messages
here.

IMHO, the only HPC area where Nocona has clear advantage over Opteron, 
is floating point applications reaching performance close to peak 
value (like Linpack). In that case it should be take into account that 
Peak_Performance = 2*frequency for both processors, and Nocona
has therefore higher values. But it's not typically for computational
chemistry.

Yours
Mikhail Kuzminsky
Zelinsky Institute of Organic Chemistry
Moscow
   




 


 
 
>
>The machine is up and running now in 64 bit mode and doing fine ;-). 
>
>Maybe the information can help you in your decision.
>
>Best regards, 
>
>Mark Somers.
>
>>Hi,
>>
>>we are going to invest some money for a few computers, and we have 
>>to
>>make a decision between the AMD-Opterons and the Intel-Nocona. 
>>What's
>>better ? We are experienced with the Opterons, but we have no idea 
>>about
>>the Noconas...
>>
>>Major codes to run on them will be classical QM packages as ADF, 
>>G03, TM,
>>some AIMD as CPMD, and possibly some classical MD as gromacs.
>>
>>Thanks,
>>Luigi
>
>-- 
>Dr. M. F. Somers
>Theoretical Chemistry - Leiden Institute of Chemistry  - Leiden 
>University
>Einsteinweg 55, P.B. 9502, 2300 RA Leiden, The Netherlands
>tel: +31715274437
>mail: m.somers|at|chem.leidenuniv.nl
>web:  http://rulgla.leidenuniv.nl/Researchers/Somers.htm
>room: HB322
>
>
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