From owner-chemistry@ccl.net Sat Oct 28 08:24:00 2006
From: "Lubos Vrbka lists]|[vrbka.net" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: Dlpoly calculation of angular momentum
Message-Id: <-32886-061028081915-27276-Go2tmmv4z0ex0XKpXuupvA+/-server.ccl.net>
X-Original-From: Lubos Vrbka <lists]-[vrbka.net>
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Date: Sat, 28 Oct 2006 21:18:53 +0900
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Sent to CCL by: Lubos Vrbka [lists=-=vrbka.net]
hi,

> I put a cluster of 55 atoms on top of alkanthiol molecule surface . The cluster is moving as a nano ball and I wanna calculate the angular momentum of this cluster with respect to time. The problem is, there is a periodic boundary and the cluster is  moving outside the boundary. The HISTORY file gives me the coordinates inside the box, so I can never know where the actual coordinates of the cluster are. How can I calculate the angular momentum of my cluster? need help...
well, i would do the following:

1) check the position of any atom of interest in every step
2) if it moves more than 1/2 of a box distance in any direction, it 
would indicate that it was wrapped and you need to add/subtract the box 
dimension to/from the respective coordinate

it is neither perfect nor efficient, but it's probably the easiest way 
how to do that (another way would be to rewrite dlpoly code not to wrap 
the coordinates). of course this works only if you write the coordinates 
frequently enough and the box is large enough, so the atoms on average 
move by much less then half of the box size.

regards,

-- 
Lubos _- -_"
http://www.lubos.vrbka.net


From owner-chemistry@ccl.net Sat Oct 28 08:59:00 2006
From: "Biju AR biju.ar(0)gmail.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL:G: optimization
Message-Id: <-32887-061028031247-8926-E5tY7DZ828U7hiJNIq1vMQ:_:server.ccl.net>
X-Original-From: "Biju AR" <biju.ar^gmail.com>
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	boundary="----=_Part_52718_15425909.1162015988539"
Date: Sat, 28 Oct 2006 11:43:08 +0530
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Sent to CCL by: "Biju AR" [biju.ar]![gmail.com]
------=_Part_52718_15425909.1162015988539
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Hello
  I am new to this field so let me take bail in advance if the question is
too simple. I tried to optimize a mono nuclear complex containing
coordinated water molecule in  *Gaussian 03 by dft method *(opt
B3LYP/extrabasis  gfoldprint POP=FULL). During optimization one of the
hydrogen from the metal coordinated water molecule detached and compound
became chemically incorrect. so i did constrain for both hydrogen( bond
length and dihedral angle) by  using molden program. but optimization
terminated with an error
Error termination request processed by link 9999.
 Error termination via Lnk1e in /usr/opt//g03/l9999.exe
So what should be the problem?. What shall  I do to get an optimized
structure?. Any information is greatly appreciated.

Thanks

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<p class="MsoNormal">Hello <br>
&nbsp; I am new to this field so let me take bail in advance if the question is
too simple. I tried to optimize a mono nuclear complex containing coordinated
water molecule in&nbsp; <strong><span style="font-weight: normal;">Gaussian 03 by
dft method</span> </strong>(<span style="color: rgb(51, 102, 255);">opt&nbsp;
B3LYP/extrabasis&nbsp; gfoldprint POP=FULL</span>). During optimization one of
the hydrogen from the metal coordinated water molecule detached and compound
became chemically incorrect. so i did constrain for both hydrogen( bond length
and dihedral angle) by&nbsp; using molden program. but optimization terminated
with an error<span style="color: rgb(51, 102, 255);"> <br>
Error termination request processed by link 9999.<br>
&nbsp;Error termination via Lnk1e in /usr/opt//g03/l9999.exe <br>
</span><span style="color: rgb(51, 51, 51);">So what should be the problem?. What
shall&nbsp; I do to get an optimized structure?. Any information is greatly
appreciated.<br>
<br>
Thanks</span></p>




------=_Part_52718_15425909.1162015988539--


From owner-chemistry@ccl.net Sat Oct 28 09:34:00 2006
From: "Tris Youngs t.youngs a qub.ac.uk" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL:G: Hyperchem and other "easy" software
Message-Id: <-32888-061027194806-5142-SzplGWhxhUG0Jo3XEfmawA]*[server.ccl.net>
X-Original-From: Tris Youngs <t.youngs%x%qub.ac.uk>
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Date: Fri, 27 Oct 2006 23:43:56 +0100 (BST)
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Sent to CCL by: Tris Youngs [t.youngs^qub.ac.uk]
As primarily a condensed-phase modeller, I agree with much of what Dr. 
Hultin says. Until recently I have conducted my research and subsequent
analysis with a combination of three or four different freeware tools 
(Molekel, gOpenMol, OpenDX etc.) but have increasingly found it rather 
tiresome to switch between them in order to get things done.

I have also not managed to find a tool that provides a regime for the 
creation of starting configurations that are of use for the simulation of 
condensed systems. For my two cents, I appreciate that Hyperchem, Spartan 
and the like offer a 'high-level' solution to computational chemistry, but 
for many researchers the use of freely-available tools is most attractive. 
As a previous contributor stated (apologies, I have forgotten exactly 
who!) the money is probably better spent on hardware on which to run free 
codes.

To depend on too many packages is, I agree, to increase the 
frustration factor, and a tool that satisfies all users will, I think, 
never be written. I myself might partially answer the call to Dr. Hultin's 
request for a (semi-altruistic) programmer, though, as I undertook the 
challenge to address just this problem (from a condensed matter point of 
view, but with a general theme) sometime earlier in the year. As a 
previous user and critic of MSI's Cerius2, I have set my standards quite high! Rest 
assured, I will inform the list if I manage to create anything I deem
worthwhile. And of course, it would be freeware.

One point I would like to make though is that I do not believe that the 
generation of code-specific commands for e.g. Gaussian, GAMESS, is of much 
importance in any modelling software. There are already tools available 
that provide interfaces to clusters, queueing systems and the like, and so 
I would suggest that providing a reasonable geometry/configuration is 
enough. The onus is then on the user to tell the code in question what to 
do with the coordinates, rather than rely on the interface to provide 
exactly what they need.

Right, that's probably about a quarter's worth....

Best regards,
Tris.

-- 
Dr. T. Youngs  (t.youngs(~)qub.ac.uk)
Atomistic Simulation Centre
Old Physics Building
Queens University Belfast
Belfast, BT7 1NN, N.I.

On Fri, 27 Oct 2006, Phil Hultin hultin++cc.umanitoba.ca wrote:

> Sent to CCL by: "Phil Hultin" [hultin _ cc.umanitoba.ca]
> This is a multi-part message in MIME format.
> 
> ------=_NextPart_000_011C_01C6F9D3.A1BB2510
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> 
> I agree with the statement that Hyperchem's primary advantage is easy use,
> and its weakness is in the actual implementation of theoretical models.
> 
>  
> 
> If you want a user-friendly interface with good computational tools, Spartan
> is probably a better choice and is in the same price range as Hyperchem.
> Even so, Spartan is by no means an ideal computational code.
> 
>  
> 
> The big problems with MOST computational freeware are 1) poor documentation
> and 2) cryptic command line interfaces.  While there are very nice freeware
> visualization tools (eg Rasmol, Molekel, Molden, SwissView) the range of
> tools for creating starting structures for computations is much more
> limited, and primarily addresses the peptide and nucleic acid communities
> (eg VMD/Molefacture).  I have also found that several programs that claim to
> be able to save structure files in a given format actually create files that
> are not readable by other programs - either because the drawing program uses
> a "dialect" of the file format, or the computational program does.  Yes, you
> can use sometimes use OpenBabel to get around this, but the frustration
> factor grows with every step you have to go through to get a usable
> structure input file.
> 
>  
> 
> There is a need for a simple, reliable and FREE option for general structure
> drawing that can save in a variety of formats.  The Marvin package from
> ChemAxon approaches this goal but it is still not quite what I have in mind.
> Such a program would create absolutely canonical 3-D structure files in MOL,
> XYZ (simple Cartesian and TINKER formats), PDB (both ATOM and HETATM/CONECT
> variants), and unique SMILES.  The Dundee PRODRG server on the web can do
> this but is not as convenient as a local program on one's own workstation or
> PC.
> 
>  
> 
> It would also be able to make input files for the common computational
> codes: Gaussian, GAMESS, MOPAC.  I know that GaussView can do this for
> Gaussian but GaussView is not free - in fact it is rather expensive.  It is
> not essential that this Freeware have all the options for these computations
> as buttons or menus, but if it can set up the structure of the file
> including the coordinate sets, and then give a command line for the user to
> type in the route section etc. that would be very convenient.  If it had
> some tools for creating z-matrices that would be a nice touch but is not as
> important as it once was.
> 
>  
> 
> Ok, so I have described what I want for Christmas.  Any altruistic
> programmers out there?
> 
>  
> 
> Dr. Philip G. Hultin
> 
> Professor of Chemistry,
> 
> University of Manitoba
> 
> Winnipeg, MB
> 
> R3T 2N2
> 
>  <mailto:hultin_._cc.umanitoba.ca> hultin_._cc.umanitoba.ca
> 
>  <http://umanitoba.ca/chemistry/people/hultin>
> http://umanitoba.ca/chemistry/people/hultin
> 
>  
> 
> 
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> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>I agree with the statement that Hyperchem&#8217;s =
> primary
> advantage is easy use, and its weakness is in the actual implementation =
> of
> theoretical models.<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>If you want a user-friendly interface with good
> computational tools, Spartan is probably a better choice and is in the =
> same
> price range as Hyperchem. &nbsp;Even so, Spartan is by no means an ideal
> computational code.<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>The big problems with MOST computational freeware are =
> 1)
> poor documentation and 2) cryptic command line interfaces.&nbsp; While =
> there
> are very nice freeware visualization tools (eg Rasmol, Molekel, Molden,
> SwissView) the range of tools for creating starting structures for =
> computations
> is much more limited, and primarily addresses the peptide and nucleic =
> acid
> communities (eg VMD/Molefacture). &nbsp;I have also found that several =
> programs
> that claim to be able to save structure files in a given format actually =
> create
> files that are not readable by other programs &#8211; either because the
> drawing program uses a &#8220;dialect&#8221; of the file format, or the
> computational program does.&nbsp; Yes, you can use sometimes use =
> OpenBabel to
> get around this, but the frustration factor grows with every step you =
> have to
> go through to get a usable structure input =
> file.<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>There is a need for a simple, reliable and FREE =
> option for general
> structure drawing that can save in a variety of formats. &nbsp;The =
> Marvin
> package from ChemAxon approaches this goal but it is still not quite =
> what I
> have in mind.&nbsp; Such a program would create absolutely canonical 3-D
> structure files in MOL, XYZ (simple Cartesian and TINKER formats), PDB =
> (both ATOM
> and HETATM/CONECT variants), and unique SMILES.&nbsp; The Dundee PRODRG =
> server
> on the web can do this but is not as convenient as a local program on =
> one&#8217;s
> own workstation or PC.<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>It would also be able to make input files for the =
> common
> computational codes: Gaussian, GAMESS, MOPAC. &nbsp;I know that =
> GaussView can
> do this for Gaussian but GaussView is not free &#8211; in fact it is =
> rather
> expensive.&nbsp; It is not essential that this Freeware have all the =
> options
> for these computations as buttons or menus, but if it can set up the =
> structure
> of the file including the coordinate sets, and then give a command line =
> for the
> user to type in the route section etc. that would be very convenient. =
> &nbsp;If
> it had some tools for creating z-matrices that would be a nice touch but =
> is not
> as important as it once was.<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>Ok, so I have described what I want for =
> Christmas.&nbsp; Any
> altruistic programmers out there?<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>Dr. Philip G. Hultin<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'>Professor of Chemistry,<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><ns0:place w:insAuthor=3D"Philip Hultin"
>  w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
>  w:endInsDate=3D"2006-10-27T13:25:00Z"><ns0:PlaceType =
> w:insAuthor=3D"Philip Hultin"
>   w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
>   w:endInsDate=3D"2006-10-27T13:25:00Z"><st1:place =
> w:st=3D"on"><st1:PlaceType
>    w:st=3D"on">University</st1:PlaceType></ns0:PlaceType></st1:place> of =
> <ns0:PlaceName
>   w:insAuthor=3D"Philip Hultin" w:insDate=3D"2006-10-27T13:25:00Z"
>   w:endInsAuthor=3D"Philip Hultin" =
> w:endInsDate=3D"2006-10-27T13:25:00Z"><st1:PlaceName
>   =
> w:st=3D"on">Manitoba</st1:PlaceName></ns0:PlaceName></ns0:place><o:p></o:=
> p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><ns0:place w:insAuthor=3D"Philip Hultin"
>  w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
>  w:endInsDate=3D"2006-10-27T13:25:00Z"><ns0:City w:insAuthor=3D"Philip =
> Hultin"
>   w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
>   w:endInsDate=3D"2006-10-27T13:25:00Z">Winnipeg</ns0:City>, <ns0:State
>   w:insAuthor=3D"Philip Hultin" w:insDate=3D"2006-10-27T13:25:00Z"
>   w:endInsAuthor=3D"Philip Hultin" =
> w:endInsDate=3D"2006-10-27T13:25:00Z">MB</ns0:State></ns0:place><o:p></o:=
> p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DFR-CA =
> style=3D'font-size:
> 10.0pt;font-family:Arial'>R3T 2N2<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><a href=3D"mailto:hultin_._cc.umanitoba.ca"><span =
> lang=3DFR-CA>hultin_._cc.umanitoba.ca</span></a></span></font><font
> size=3D2 face=3DArial><span lang=3DFR-CA =
> style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
> >
> 
> <p class=3DMsoNormal><font size=3D2 face=3DArial><span =
> style=3D'font-size:10.0pt;
> font-family:Arial'><a =
> href=3D"http://umanitoba.ca/chemistry/people/hultin"><span
> lang=3DFR-CA>http://umanitoba.ca/chemistry/people/hultin</span></a></span=
> ></font><font
> size=3D2 face=3DArial><span lang=3DFR-CA =
> style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
> >
> 
> <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
> lang=3DFR-CA
> style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>
> 
> </div>
> 
> </body>
> 
> </html>
> 
> ------=_NextPart_000_011C_01C6F9D3.A1BB2510--> 
> 
>


From owner-chemistry@ccl.net Sat Oct 28 12:19:00 2006
From: "T-Tsuru coral t-tsuru^^^coral.dti.ne.jp" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: MO energy and number of molecules
Message-Id: <-32889-061028121637-22005-8OAaa+dQT0difPikYxssVg*server.ccl.net>
X-Original-From: "T-Tsuru coral" <t-tsuru ~ coral.dti.ne.jp>
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Sent to CCL by: "T-Tsuru coral" [t-tsuru#%#coral.dti.ne.jp]

Hello, CCLers.

I have two questions of MO energy concerning the number of molecules.

I got interested in the MO energy distribution of assembled molecules, when I developed 
following SWF(a toy Flash movie!) which shows MO energies (EigenValues) of both H2O 
monomer and dimmer.
[SWF] http://yu-net.info/swfup/viewswf.php/5366.swf
   
  ** The calculation is done by MOPAC2000 (c) Fujitsu and the method is PM3 using EF 
      optimization.
  ** You can see the MO energies by [EV] bottom and see the numerical data by 
     [Data] bottom. And you can drag and move the molecules. When you press [Data] 
     bottom again, the numerical data will disappears. If you want to replay this SWF, 
     please reload the HP.
  ### Advertisement and Japanese message of uploader should be ignore :-)  

Highest MO energy and lowest MO energy are nearly equal (5.33/5.03 and -36.82/-37.28). 
And HOMO-LUMO energy are nearly equal too (4.05/3.64 and -12.31/-11.91). But the 
number of MO energy is increased nearly double (6 ---> 11) and each MO energy seems to 
be increased double ([example] monomer No.2: -17.57  --->  dimmer No.3 and No.4).

So I have following two questions.
Q1) The dimmer's two H2O are same molecule. Why is the number of MO energies increased 
     nearly double?
Q2) (Concerning above) Why does monomer's each MO energy seem to be increased double? 
     (Why can't be dimmer's two MO energies united to one? ) 

Some books which describe solid material's energy show the increase of energy-level number 
by the number of atoms. But these books don't describe the reason of this increase.

If you know any hint of above two questions, please teach me.
When I receive the replies, I will summarize them and send to CCL.



Thanks.
----------------------------------------------------
      Telkuni Tsuru     t-tsuru .. coral.dti.ne.jp
           Bunshi Gijyutu


From owner-chemistry@ccl.net Sat Oct 28 15:06:01 2006
From: "William F. Coleman wcoleman[a]wellesley.edu" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: MO energy and number of molecules
Message-Id: <-32890-061028132538-25451-Uj6u1xuuXFit4iDDL/XMOQ]*[server.ccl.net>
X-Original-From: "William F. Coleman" <wcoleman:+:wellesley.edu>
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Date: Sat, 28 Oct 2006 12:49:11 -0400
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Sent to CCL by: "William F. Coleman" [wcoleman[a]wellesley.edu]
"CCL Subscribers" <chemistry]|[ccl.net> on Saturday, October 28, 2006 at
12:25 PM -0500 wrote:
>Q1) The dimmer's two H2O are same molecule. Why is the number of MO
>energies increased 
>     nearly double?
>Q2) (Concerning above) Why does monomer's each MO energy seem to be
>increased double? 
>     (Why can't be dimmer's two MO energies united to one? ) 

The total number of MOs will be equal to the total number of basis
orbitals used.  You have used a basis set that in atomic orbital terms
could be labeled as a 1s function on each hydrogen and a 2s and 3 2p
functions on the oxygen, for a total of six functions for the water
molecule.  In the transition for atomic to molecular functions, the number
of functions must be conserved - if you think of these as orbitals, the
number of molecular orbitals mu equal the number of atomic orbitals used
in the calculation.  With two water molecules you will have twice as many
MOs.

There is no evidence of the distance between the water molecules in your
dimer, but you would expect that if the distance was very large, the MOs
on one water would not interact with those on the other, and you would
have two sets of identical, non-interacting, MOs.  As you bring the two
molecules closer (and optimize the configuration of the dimer) you would
find more interaction between the MOs on the individual waters, and some
changes in the energy, but those changes will never be huge.

Hope this helps.

Cheers,

Flick Coleman
_______________
William F. Coleman
Professor and Chair, Department of Chemistry
Wellesley College
Wellesley, MA 02481

email:      wcoleman]|[wellesley.edu
web:       www.wellesley.edu/Chemistry/colemanw.html
voice:     781-283-3129
fax:        781-283-3642

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