From owner-chemistry@ccl.net Mon Apr 21 07:51:01 2008
From: "Steve Williams willsd##appstate.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: Learning Computational
Message-Id: <-36792-080421074446-13586-svXZwdQI39fN6wXq1Nr7gQ[A]server.ccl.net>
X-Original-From: Steve Williams <willsd++appstate.edu>
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Date: Mon, 21 Apr 2008 07:37:09 -0400
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Sent to CCL by: Steve Williams [willsd : appstate.edu]
Since Gaussian is a tool that you have available, I'd suggest getting a 
copy of "Exploring Chemistry with Electronic Structure Methods" by 
Foresman and Frisch.  It covers many topics related to practical 
applications of quantum chemistry methods and is written with Gaussian 
in mind, but certainly could be used with other ab initio programs, 
assuming you already know how to construct inputs for those programs.
Steve Williams


Amin Ordikhani-Seyedlar a.ordikhani/agmail.com wrote:
> Sent to CCL by: "Amin  Ordikhani-Seyedlar" [a.ordikhani:_:gmail.com]
> Hi all,
> apologize me for taking your time with my low level question. I'm a master student of analytical chemistry but really keen to learn computational (as it is so powerful). I have some beginner experiments on Gaussian03. I wanna predict the behaviour of molecules in different situations and ...
> I wanna ask you if you were me how you would start learning? There is no one in my university that can help me so I have to learn from books and also CCL really helps me.
> Thanks in advance.>
>
>


From owner-chemistry@ccl.net Mon Apr 21 09:49:01 2008
From: "nee MI neerajmisra||hotmail.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL:G: gaussian output
Message-Id: <-36793-080421094702-17723-MALuV7h3CRcpMuzwf6Iv7g.@.server.ccl.net>
X-Original-From: "nee  MI" <neerajmisra++hotmail.com>
Date: Mon, 21 Apr 2008 09:46:59 -0400


Sent to CCL by: "nee  MI" [neerajmisra[#]hotmail.com]
THE GAUSSIAN OUTPUT (OPTIMIZATION+FREQ) BY B3LYP(6-311)G(d,p) SHOWS A DIFFERENT STRUCTURE(IN TERMS OF BONDING) AS COMPARED TO THE INPUT.

CAN THIS BE EXPLAINED?


From owner-chemistry@ccl.net Mon Apr 21 10:24:01 2008
From: "Ariza Ahmad nriza|-|hotmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL:G: how to find binding energy in Gaussian output
Message-Id: <-36794-080421043415-32155-7jq+J5JjBhj9qQY+IcucEw-x-server.ccl.net>
X-Original-From: "Ariza  Ahmad" <nriza : hotmail.com>
Date: Mon, 21 Apr 2008 04:34:11 -0400


Sent to CCL by: "Ariza  Ahmad" [nriza#hotmail.com]
Hello all,
I have a problems with my Gaussian output
I am really new to Gaussian.
I have done a calculation in Gaussian
Now I need to get the binding energy
But I don't know how to get it.
Can anyone teach me on that?


From owner-chemistry@ccl.net Mon Apr 21 10:58:00 2008
From: "faza##uvigo.es" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: Learning Computational
Message-Id: <-36795-080421045208-1018-R3zHl4Aet/WSrAt37V9ZcA##server.ccl.net>
X-Original-From: faza-$-uvigo.es
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Sent to CCL by: faza^^^uvigo.es

Hi!
As other people have said, the advice on how to learn computational =20
chemistry can change a lot depending in your main area of interest =20
(meaning what you want to model). My very general suggestions from the =20
organic chemist/biochemist point of view are the books I collected in =20
the following list in amazon (under my name and the title Learning =20
Comp. Chem., if the link does not work):
http://www.amazon.com/gp/registry/wishlist/1GFZN22OFAUJW/ref=3Dcm_wl_rlist_g=
o

 From them I would choose Tamar Schlick's book if you are more =20
oriented towards the modeling of biological molecules, and Cramer=B4s =20
for anything else. In fact, I would choose both in any case, but time =20
and other resources are sometimes limited...

I wish you well in your endeavour.

Regards,

Olalla Nieto



"Amin Ordikhani-Seyedlar a.ordikhani/a\gmail.com" =20
<owner-chemistry[A]ccl.net> escribiu:

>
> Sent to CCL by: "Amin  Ordikhani-Seyedlar" [a.ordikhani:_:gmail.com]
> Hi all,
> apologize me for taking your time with my low level question. I'm a  =20
> master student of analytical chemistry but really keen to learn  =20
> computational (as it is so powerful). I have some beginner  =20
> experiments on Gaussian03. I wanna predict the behaviour of  =20
> molecules in different situations and ...
> I wanna ask you if you were me how you would start learning? There  =20
> is no one in my university that can help me so I have to learn from  =20
> books and also CCL really helps me.
> Thanks in advance.


From owner-chemistry@ccl.net Mon Apr 21 11:33:01 2008
From: "faza^uvigo.es" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: gaussian output
Message-Id: <-36796-080421103515-13355-qj8hBybcH91rCkkPcsiivA##server.ccl.net>
X-Original-From: faza|-|uvigo.es
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Date: Mon, 21 Apr 2008 16:34:59 +0200
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Sent to CCL by: faza|-|uvigo.es
Hi!
I don't know what you are calling "bonding" in your input and output, =20
so I will assume that you are using a visualization tool (gaussview, =20
molden, molekel...) and saying that there is a bond between two atoms =20
when the program draws a line between them. Forgive me then if I am =20
wrong and your problem is another.

Most programs do that as a function of the distance between two atoms, =20
so that, if (my numbers are completely made up) two carbons are =20
separated any distance up to 2.6 A, a bond will be drawn and no bond =20
will appear for longer distances. This doesn't have to correlate with =20
the existence or not of a "real" bond between those atoms (although it =20
usually does, and that's why they work like that).
Thus, even for geometry optimizations when there is no bond forming or =20
bond breaking, sometimes you "see" a bond disappearing if it is a =20
little more stretched than usual (common when studying organometallic =20
compounds). Another thing that can be happening is that you have a =20
starting geometry that is not very good or stable (or you have a very =20
low reaction barrier) so that during the optimization bonds are really =20
being formed or broken and you obtain a different compound.
Your problem (and it might not be a problem) can be any of those.

Kind regards,

Olalla Nieto

P.S. You have to take into account that when using ab-initio methods, =20
unlike molecular mechanic methods based in force fields, the atoms are =20
described solely as positively charged nuclei and a surrounding cloud =20
of electrons, so the only input you need to determine a molecular =20
geometry are the positions of the nuclei (no bond parameters or =20
bonding patterns).


"nee MI neerajmisra||hotmail.com" <owner-chemistry/./ccl.net> escribiu:

>
> Sent to CCL by: "nee  MI" [neerajmisra[#]hotmail.com]
> THE GAUSSIAN OUTPUT (OPTIMIZATION+FREQ) BY B3LYP(6-311)G(d,p) SHOWS  =20
> A DIFFERENT STRUCTURE(IN TERMS OF BONDING) AS COMPARED TO THE INPUT.
>
> CAN THIS BE EXPLAINED?
>
>
>


From owner-chemistry@ccl.net Mon Apr 21 12:08:00 2008
From: "Eduard Matito ematito]-[gmail.com" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: Learning Computational
Message-Id: <-36797-080421105716-29771-BD4hHRCAZ8uGtGeniPptCA-,-server.ccl.net>
X-Original-From: Eduard Matito <ematito*gmail.com>
Content-Type: multipart/alternative; boundary=Apple-Mail-4-698045792
Date: Mon, 21 Apr 2008 15:53:16 +0200
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Sent to CCL by: Eduard Matito [ematito*gmail.com]

--Apple-Mail-4-698045792
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The next two are also very suitable for getting a grasp into  
different topics:
- Introduction to Computational Chemistry, 2nd Ed. by Frank Jensen  
(Wiley)
- Essentials of Computational Chemistry, 2nd. Ed. by Christopher J  
Cramer (Wiley)
Eduard

>> I wanna ask you if you were me how you would start learning? There  
>> is no one in my university that can help me so I have to learn  
>> from books and also CCL really helps me.
>>

--
Eduard Matito
Postdoctoral Researcher
Lundbeck Foundation, Center for Theoretical Chemistry
University of Aarhus, Aarhus (Denmark)
http://lctc.dcmedia.dk/index.php?id=77




--Apple-Mail-4-698045792
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<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">
The next two are also very suitable for getting a grasp into different =
topics:=A0<div>- Introduction to Computational Chemistry, 2nd Ed. by =
Frank Jensen (Wiley)</div><div>- Essentials of Computational Chemistry, =
2nd. Ed. by Christopher J Cramer =
(Wiley)</div><div>Eduard</div><div><div><html><br></html><blockquote =
type=3D"cite"><blockquote type=3D"cite"><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I wanna ask =
you if you were me how you would start learning? There is no one in my =
university that can help me so I have to learn from books and also CCL =
really helps me.</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; =
"><br></div></blockquote></blockquote></div><div> <span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; color: =
rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: =
normal; font-variant: normal; font-weight: normal; letter-spacing: =
normal; line-height: normal; orphans: 2; text-align: auto; text-indent: =
0px; text-transform: none; white-space: normal; widows: 2; word-spacing: =
0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; -webkit-border-horizontal-spacing: =
0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); =
font-family: Helvetica; font-size: 18px; font-style: normal; =
font-variant: normal; font-weight: normal; letter-spacing: normal; =
line-height: normal; -webkit-text-decorations-in-effect: none; =
text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; =
orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; =
-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: =
0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; =
font-style: normal; font-variant: normal; font-weight: normal; =
letter-spacing: normal; line-height: normal; =
-webkit-text-decorations-in-effect: none; text-indent: 0px; =
-webkit-text-size-adjust: auto; text-transform: none; orphans: 2; =
white-space: normal; widows: 2; word-spacing: 0px; "><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font-size: 12px; ">--</div><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: =
12px; "><span class=3D"Apple-style-span" style=3D"font-size: 12px; =
">Eduard Matito</span></div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><span =
class=3D"Apple-style-span" style=3D"font-size: 12px; ">Postdoctoral =
Researcher</span></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><span =
class=3D"Apple-style-span" style=3D"font-size: 12px; ">Lundbeck =
Foundation, Center for Theoretical Chemistry</span></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font-size: 12px; "><span class=3D"Apple-style-span" =
style=3D"font-size: 12px; ">University of Aarhus, Aarhus =
(Denmark)</span></div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font-size: 12px; "><span =
class=3D"Apple-style-span" style=3D"font-size: 12px; "><a =
href=3D"http://lctc.dcmedia.dk/index.php?id=3D77">http://lctc.dcmedia.dk/i=
ndex.php?id=3D77</a></span></div><br =
class=3D"Apple-interchange-newline"></span></span></span><br =
class=3D"Apple-interchange-newline"> </div><br></div></body></html>=

--Apple-Mail-4-698045792--


From owner-chemistry@ccl.net Mon Apr 21 12:54:01 2008
From: "Pascal Boulet pascal.boulet-#-univ-provence.fr" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: how to find binding energy in Gaussian output
Message-Id: <-36798-080421120138-16407-QuKSqZxmP6eNBtpAg4VqBg(0)server.ccl.net>
X-Original-From: Pascal Boulet <pascal.boulet%%univ-provence.fr>
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Date: Mon, 21 Apr 2008 17:24:35 +0200
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Sent to CCL by: Pascal Boulet [pascal.boulet#,#univ-provence.fr]

Hello Ariza,

Well, if I understand correctly your problem, you have to calculate the 
energy of each fragments separately and use the following equation :
E(binding) = E (whole system) - [E(fragment 1)+E(fragment 2) + ... 
+E(fragment n)]

Hope this helps,
Pascal

Ariza Ahmad nriza|-|hotmail.com wrote:
> Sent to CCL by: "Ariza  Ahmad" [nriza#hotmail.com]
> Hello all,
> I have a problems with my Gaussian output
> I am really new to Gaussian.
> I have done a calculation in Gaussian
> Now I need to get the binding energy
> But I don't know how to get it.
> Can anyone teach me on that?>
>
>   

-- 
Dr. Pascal Boulet, Computational Chemist
University of Provence
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, case MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: pascal.boulet ~~ univ-provence.fr
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet


From owner-chemistry@ccl.net Mon Apr 21 13:32:00 2008
From: "Ashish Datt ashish_cares!^!hotmail.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL:G: Input files for QM/MM in zeolites
Message-Id: <-36799-080421133010-24670-fERyfjLPxPNO2qabIwzvWw_._server.ccl.net>
X-Original-From: "Ashish  Datt" <ashish_cares++hotmail.com>
Date: Mon, 21 Apr 2008 13:30:06 -0400


Sent to CCL by: "Ashish  Datt" [ashish_cares::hotmail.com]
hello

Could anybody send me sone attachments where i can look up for soem input files for the gaussian software that has QM/MM calculations on zeolites.

Thanks and Regards
Ashish Datt


From owner-chemistry@ccl.net Mon Apr 21 15:16:00 2008
From: "Raja S r.subramanian(0)ipc.uni-stuttgart.de" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL:G: Electri field gradient
Message-Id: <-36800-080421120404-19075-kdWw+u8xlPskR7i+9T8E0g_-_server.ccl.net>
X-Original-From: "Raja  S" <r.subramanian_-_ipc.uni-stuttgart.de>
Date: Mon, 21 Apr 2008 12:04:00 -0400


Sent to CCL by: "Raja  S" [r.subramanian a ipc.uni-stuttgart.de]
Dear everyone,
I need to know some small details regarding EFG calculation. When we make geometry optimization by Gaussian03, one will get the optimized structure alone with 'Quadrupole moment in Debye-Ang'...it looks like this, see below:
Quadrupole moment (field-independent basis, Debye-Ang):
   XX=    -4.9686   YY=    -5.1891   ZZ=    -5.2730
   XY=     0.0374   XZ=    -0.0229   YZ=     0.0553
 Traceless Quadrupole moment (field-independent basis, Debye-Ang):
   XX=     0.1750   YY=    -0.0455   ZZ=    -0.1294
   XY=     0.0374   XZ=    -0.0229   YZ=     0.0553
in the above two moments which is EFG (Vxx, Vyy, and Vzz) ????or how to calculate EFG???
advance thanks,
raja.


From owner-chemistry@ccl.net Mon Apr 21 15:51:00 2008
From: "William F. Polik polik/./hope.edu" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL:G: how to find binding energy in Gaussian output
Message-Id: <-36801-080421153855-15599-Xi4btNh2lhk5j8zpYTGeHQ~~server.ccl.net>
X-Original-From: "William F. Polik" <polik+*+hope.edu>
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Date: Mon, 21 Apr 2008 14:22:15 -0400
Mime-Version: 1.0


Sent to CCL by: "William F. Polik" [polik::hope.edu]
For accurate calculation of the binding energy, you will want to make 
a "counterpoise correction" (which accounts for basis set 
superposition error) and also account for different zero-point energy 
of the fragments and entire system.

See
   http://qcl.theochem.tu-muenchen.de/qcl/help/counterpoise_e.html
for an explanation.

Will Polik

At 11:24 AM 4/21/2008, you wrote:

>Sent to CCL by: Pascal Boulet [pascal.boulet#,#univ-provence.fr]
>
>Hello Ariza,
>
>Well, if I understand correctly your problem, you have to calculate 
>the energy of each fragments separately and use the following equation :
>E(binding) = E (whole system) - [E(fragment 1)+E(fragment 2) + ... 
>+E(fragment n)]
>
>Hope this helps,
>Pascal
>
>Ariza Ahmad nriza|-|hotmail.com wrote:
>>Sent to CCL by: "Ariza  Ahmad" [nriza#hotmail.com]
>>Hello all,
>>I have a problems with my Gaussian output
>>I am really new to Gaussian.
>>I have done a calculation in Gaussian
>>Now I need to get the binding energy
>>But I don't know how to get it.
>>Can anyone teach me on that?>
>>
>>
>
>--
>Dr. Pascal Boulet, Computational Chemist
>University of Provence
>Laboratoire Chimie Provence, UMR6264
>Centre Saint-Jerome, case MADIREL
>F-13397 MARSEILLE Cedex 20, France
>Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
>courriel: pascal.boulet,,univ-provence.fr
>http://www.lc-provence.fr
>http://allos.up.univ-mrs.fr/boulet
>


From owner-chemistry@ccl.net Mon Apr 21 22:55:01 2008
From: "Ariza Ahmad nriza- -hotmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Helps on Molecular Dynamics
Message-Id: <-36802-080421225148-28483-FTT/jzTaM4V1Jhu/A8Neyw]_[server.ccl.net>
X-Original-From: "Ariza  Ahmad" <nriza^_^hotmail.com>
Date: Mon, 21 Apr 2008 22:51:44 -0400


Sent to CCL by: "Ariza  Ahmad" [nriza^_^hotmail.com]
Hi All,
I am new to Molecular Dynamic simulations.
Actually I'm using Fortran in Linux for the simulations
Now I need to find an MD software for Windows XP operating system
Is there any? I found Gromacs which I think can be installed on both Linux and Windows system.But I dont know how to install in Windows. Could anyone please help me..or giving some ideas?

Thank you very much!


From owner-chemistry@ccl.net Mon Apr 21 23:29:01 2008
From: "Tiejun Cheng tjcheng.:.mail.sioc.ac.cn" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: How to implement your own Daylight or MACCS fingerprint?
Message-Id: <-36803-080421223653-27296-pLqRcnHTSUQpYoTFrPWzfg,,server.ccl.net>
X-Original-From: "Tiejun  Cheng" <tjcheng[-]mail.sioc.ac.cn>
Date: Mon, 21 Apr 2008 22:36:49 -0400


Sent to CCL by: "Tiejun  Cheng" [tjcheng:_:mail.sioc.ac.cn]
Hi all,

Anyone know or any clue on how to implement the Daylight or MACCS fingerprint? These two are very useful.

Sincerely,

Jay