From owner-chemistry@ccl.net Wed Dec  7 00:33:00 2011
From: "Muhammad Khaled Tumbi khaledtumbi(0)gmail.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: MD Simulations
Message-Id: <-46001-111207003133-21318-+4ZjaptIjBvKQ6Z7i0CcvQ()server.ccl.net>
X-Original-From: Muhammad Khaled Tumbi <khaledtumbi##gmail.com>
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Date: Wed, 7 Dec 2011 11:01:07 +0530
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Sent to CCL by: Muhammad Khaled Tumbi [khaledtumbi,gmail.com]
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Content-Type: text/plain; charset=ISO-8859-1

Hi,
for CPMD and VASP
i recommend the book entitled
"Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods"
http://www.amazon.com/Ab-Initio-Molecular-Dynamics-Advanced/dp/0521898633
<http://www.amazon.com/Ab-Initio-Molecular-Dynamics-Advanced/dp/0521898633>

On Wed, Dec 7, 2011 at 2:16 AM, Sanjay Bharathwaj computationalchemist-.-
gmail.com <owner-chemistry|*|ccl.net> wrote:

> Dear All,
>
> Many thanks for the response.
>
> What i am looking for is to carry out
> a systematic study on the materials using VASP.
>
> May be a short introduction of what is the difference between
> ab-inito MD and a CPMD, and how to decide which one
> to choose for a particular system would be great.
>
> Also, if you have any tutorials for VASP/CASTEP
> on handling these simulations for a surfaces with a molecule
> on it would be really helpful.
>
> Does any one have this.
>
> Best regards,
> Sanjay
>
> On 6 December 2011 17:09, Sanjay Bharathwaj computationalchemist/./
> gmail.com <owner-chemistry%a%ccl.net <owner-chemistry%25a%ccl.net>> wrote:
>
>>
>> Dear Sir,
>>
>> I am new to molecular dynamics and
>> i wish to understand it before i can start working on it.
>>
>> In this regard, does anyone can point me to the
>> tutorials on various kinds of MD available and
>> theoretical background.
>>
>> Best regards,
>> Sanjay
>>
>>
>>
>> --
>> Regards,
>> Dr. Sanjay Bharathwaj Kumar,
>> Dharmendra Institute of Technology,
>> India.
>>
>
>
>
> --
> Regards,
> Dr. Sanjay Bharathwaj Kumar,
> Dharmendra Institute of Technology,
> India.
>



-- 
Tumbi Muhammed Khaled Abdul Waheed,
Research Scholar,
Department Of Pharmacoinformatics,
NIPER, S.A.S. Nagar, Mohali,
Punjab, India.
Mob. +91 78145 24855
www.niper.ac.in

--0016e6506b1c1482e104b379ddfc
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Hi,<div>for CPMD and VASP</div><div>i recommend the book=A0entitled</div><d=
iv>&quot;<span class=3D"Apple-style-span" style=3D"font-size: 26px; font-we=
ight: bold; ">Ab Initio Molecular Dynamics: Basic Theory and Advanced Metho=
ds</span>&quot;</div>

<div><a href=3D"http://www.amazon.com/Ab-Initio-Molecular-Dynamics-Advanced=
/dp/0521898633">http://www.amazon.com/Ab-Initio-Molecular-Dynamics-Advanced=
/dp/0521898633=A0</a><br><br><div class=3D"gmail_quote">On Wed, Dec 7, 2011=
 at 2:16 AM, Sanjay Bharathwaj computationalchemist-.-<a href=3D"http://gma=
il.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemist=
ry|*|ccl.net">owner-chemistry|*|ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">Dear All,<div><br></div><div>Many thanks fo=
r the response.</div><div><br></div><div>What i am looking for is to carry =
out</div>

<div>a systematic study on the materials using VASP.</div><div><br></div><d=
iv>May be a short introduction of what is the difference between</div>
<div>ab-inito MD and a CPMD, and how to decide which one</div><div>to choos=
e for a particular system would be great.</div><div><br></div><div>Also, if=
 you have any tutorials for VASP/CASTEP</div><div>on handling these simulat=
ions for a surfaces with a molecule</div>


<div>on it would be really helpful.=A0</div><div><br></div><div>Does any on=
e have this.</div><div><br></div><div>Best regards,</div><div>Sanjay</div><=
div class=3D"HOEnZb"><div class=3D"h5"><div><br></div><div><div class=3D"gm=
ail_quote">

On 6 December 2011 17:09, Sanjay Bharathwaj computationalchemist/./<a href=
=3D"http://gmail.com" target=3D"_blank">gmail.com</a> <span dir=3D"ltr">&lt=
;<a href=3D"mailto:owner-chemistry%25a%ccl.net" target=3D"_blank">owner-che=
mistry%a%ccl.net</a>&gt;</span> wrote:<br>


<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><br clear=3D"all"><div><span style=3D"border=
-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Dear Sir,<d=
iv>


<br>
</div><div>I am new to molecular dynamics and=A0</div><div>i wish to unders=
tand it before i can start working on it.</div><div><br></div><div>In this =
regard, does anyone can point me to the</div><div>tutorials on various kind=
s of MD available and=A0</div>



<div>theoretical background.=A0</div><div><br></div><div>Best regards,</div=
><div>Sanjay<br clear=3D"all"></div><div><br></div><div><br></div><div><br>=
</div></span></div><font color=3D"#888888">-- <br>Regards,<br>Dr. Sanjay Bh=
arathwaj Kumar,<br>


Dharmendra Institute of Technology,<br>
India.<br>
</font></blockquote></div><br><br clear=3D"all"><div><br></div>-- <br>Regar=
ds,<br>Dr. Sanjay Bharathwaj Kumar,<br>Dharmendra Institute of Technology,<=
br>India.<br>
</div>
</div></div></blockquote></div><br><br clear=3D"all"><div><br></div>-- <br>=
Tumbi Muhammed Khaled Abdul Waheed,<br>Research Scholar,<br>Department Of P=
harmacoinformatics,<br>NIPER, S.A.S. Nagar, Mohali,<br>Punjab, India.<div>

Mob. +91 78145 24855<br><a href=3D"http://www.niper.ac.in" target=3D"_blank=
">www.niper.ac.in</a></div><br>
</div>

--0016e6506b1c1482e104b379ddfc--


From owner-chemistry@ccl.net Wed Dec  7 02:43:00 2011
From: "bonoit bonoit bonoit_10/./yahoo.fr" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Periodic table of elements
Message-Id: <-46002-111207024225-26040-6l+TFZvPKi2BSfDnip6BaQ-#-server.ccl.net>
X-Original-From: "bonoit  bonoit" <bonoit_10,,yahoo.fr>
Date: Wed, 7 Dec 2011 02:42:23 -0500


Sent to CCL by: "bonoit  bonoit" [bonoit_10()yahoo.fr]
Dear CClers,

i have some questions about the Periodic table of elements;
1-Is the formulae ns2 (n-1)dx (x inferior or equal to 8)correct for determining the transition elements?

2-Whay, when we an electronic configuration like 4s2 3d10 4p2 (valence electron for Ge), we mention 3d10 as valence electron and in this case we have only 4s2 4p2? what is the reason for excluding 3d10?

Thank you in advance
Sincerely,
Bonoit


From owner-chemistry@ccl.net Wed Dec  7 03:21:01 2011
From: "Michel Petitjean petitjean.chiral(-)gmail.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: citation style
Message-Id: <-46003-111207031840-1282-Yg9fpY1MJl5eta30SqNE9g!^!server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral(~)gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 7 Dec 2011 09:18:32 +0100
MIME-Version: 1.0


Sent to CCL by: Michel Petitjean [petitjean.chiral=-=gmail.com]
Dear Abhishek,
Bannish Word, Endnote, etc. Most of your problems will be solved with
using latex, bibtex.
Also, bannish Windows PCs. Use linux, or eventually macosx.
Sincerely,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral-,-gmail.com (preferred),
michel.petitjean-,-univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2011/12/6 ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com
<owner-chemistry-,-ccl.net>:
> Dear CCL members,
>
>       This question regards to citation style. I'm about to finish a paper
> for a journal (Journal of Molecular structure:theochem).As you know it is
> painful to write 50 or more references manually and manage them. I am
> mendeley user but this citation style is not there in mendeley repo ( use
> .csl extension). I have the citation style for Endnote (.ens extension). So
> need a help to write my citation in above journal format. Please suggest the
> easiest way. Is there  any way to convert the .ens to .csl or any valuable
> suggestion from your side. I will be grateful to you. Thank you.
>
>
>
> ****************************************************
>
>  ABHISHEK SHAHI
>
> Research Scholar
> Inorganic and Physical Chemistry
> Indian Institute Of Science
> Bangalore-12
> E-mail:                  shahi]~[ipc.iisc.ernet.in
>                                 shahi.abhishek1984]~[gmail.com
>
>
> *****************************************************
>


From owner-chemistry@ccl.net Wed Dec  7 05:12:01 2011
From: "Vincent Leroux vincent.leroux*_*loria.fr" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: citation style
Message-Id: <-46004-111207044347-12747-FWMCCfQjw99NiXxqmOuQ6g+*+server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux:-:loria.fr>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Wed, 07 Dec 2011 10:43:30 +0100
MIME-Version: 1.0


Sent to CCL by: Vincent Leroux [vincent.leroux[*]loria.fr]

Well, there is an easy solution. Select all the citations you wish to 
use from Mendeley, and export them as "Endnote XML". Then import the 
resulting XML file into EndNote, and use it as usual. This works the 
other way, too.

Note: you may consider dropping out EndNote and Word, as Michel 
suggested, because these programs are instruments of torture, but going 
for BibTex/LaTeX/Linux at the present time may also be going straight to 
hell with good intents. I am especially thinking of the situation where 
you are working with colleagues on a paper: you may not be very popular 
if you try to enforce using LaTeX to others, and you will probably end 
up doing more work than needed if as the main author you stick yourself 
to it while others keep using what they are used to (and they will!). 
Good news for you: more citation styles and better integration with 
Word/OpenOffice/etc. is one of the current development priorities for 
Mendeley. We may eventually be able to trash EndNote for good soon... 
(next shall be Word! one step at a time...)


On 06/12/2011 21:32, ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com wrote:
> Dear CCL members,
>
>        This question regards to citation style. I'm about to finish a
> paper for a journal (Journal of Molecular structure:theochem).As you
> know it is painful to write 50 or more references manually and manage
> them. I am mendeley user but this citation style is not there in
> mendeley repo ( use .csl extension). I have the citation style for
> Endnote (.ens extension). So need a help to write my citation in above
> journal format. Please suggest the easiest way. Is there  any way to
> convert the .ens to .csl or any valuable suggestion from your side. I
> will be grateful to you. Thank you.
>
>
>
> ****************************************************
>
> *ABHISHEK SHAHI*
>
> /Research Scholar
> Inorganic and Physical Chemistry
> Indian Institute Of Science
> Bangalore-12/
> E-mail: shahi]~[ipc.iisc.ernet.in <mailto:shahi]~[ipc.iisc.ernet.in>
> shahi.abhishek1984]~[gmail.com <mailto:shahi.abhishek1984]~[gmail.com>
> *
> *
> *****************************************************
>


From owner-chemistry@ccl.net Wed Dec  7 07:23:01 2011
From: "Sebastian Kozuch kozuchs]*[yahoo.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: citation style
Message-Id: <-46005-111207072151-2459-qFv0TIJHhIxwjjZSkARjOA%x%server.ccl.net>
X-Original-From: Sebastian Kozuch <kozuchs%%yahoo.com>
Content-Transfer-Encoding: 8bit
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Date: Wed, 7 Dec 2011 04:21:44 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Sebastian Kozuch [kozuchs###yahoo.com]


I know it's not a computational chemistry topic, but it is a matter of everyday use for all scientists. So I'm interested to know the opinion of people with experience on reference software.
I don't have Endnote, and I will not pay for it. However, I made a pact with the devil, so I use Windows and Word.
I use Zotero for references, which is free but has a couple of issues, most important one is that it works only inside firefox (not a problem for me). I am happy with it. Once I didn't have the reference format of one particular journal, but I managed to build it based on another similar style.

Endnote web is for free, but last time I tried it was quite useless. Bibtex is for latex, and I will not learn latex. Period. (It is not my intention to start a public debate on latex vs. word).

What about Mendeley? Did someone tried Qiqqa? Another option that comes to your mind?


Best,

Sebastian Kozuch



________________________________
> From: Michel Petitjean petitjean.chiral(-)gmail.com <owner-chemistry|ccl.net>
To: "Kozuch, Sebastian " <kozuchs|yahoo.com> 
Sent: Wednesday, December 7, 2011 10:18 AM
Subject: CCL: citation style


Sent to CCL by: Michel Petitjean [petitjean.chiral=-=gmail.com]
Dear Abhishek,
Bannish Word, Endnote, etc. Most of your problems will be solved with
using latex, bibtex.
Also, bannish Windows PCs. Use linux, or eventually macosx.
Sincerely,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral _ gmail.com (preferred),
michel.petitjean _ univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2011/12/6 ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com
<owner-chemistry _ ccl.net>:
> Dear CCL members,
>
>       This question regards to citation style. I'm about to finish a paper
> for a journal (Journal of Molecular structure:theochem).As you know it is
> painful to write 50 or more references manually and manage them. I am
> mendeley user but this citation style is not there in mendeley repo ( use
> .csl extension). I have the citation style for Endnote (.ens extension). So
> need a help to write my citation in above journal format. Please suggest the
> easiest way. Is there  any way to convert the .ens to .csl or any valuable
> suggestion from your side. I will be grateful to you. Thank you.
>
>
>
> ****************************************************
>
>  ABHISHEK SHAHI
>
> Research Scholar
> Inorganic and Physical Chemistry
> Indian Institute Of Science
> Bangalore-12
> E-mail:                  shahi]~[ipc.iisc.ernet.in
>                                 shahi.abhishek1984]~[gmail.com
>
>
> *****************************************************http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt                        


From owner-chemistry@ccl.net Wed Dec  7 07:58:00 2011
From: "Phil Hasnip phil.hasnip _ york.ac.uk" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: MD Simulations
Message-Id: <-46006-111207073552-7965-3Xdoz+L4w2wD0q7izP9Jbw^^^server.ccl.net>
X-Original-From: Phil Hasnip <phil.hasnip^_^york.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Wed, 7 Dec 2011 12:40:26 +0000 (GMT)
MIME-Version: 1.0


Sent to CCL by: Phil Hasnip [phil.hasnip[A]york.ac.uk]
Dear Sanjay,

> Also, if you have any tutorials for VASP/CASTEP on handling these 
> simulations for a surfaces with a molecule on it would be really 
> helpful.

I can't help with VASP I'm afraid beyond what is common to all ab initio 
MD programs, but I'd be more than happy to provide any CASTEP help you 
might need. You've probably read this already, but if not look at:

   http://www.castep.org

and go to "Documentation" on the left-hand links panel. There are two 
tutorials on MD in CASTEP, and a link to the CASTEP manual by Accelrys and 
a lot of other useful documentation.

One of the most important first steps is to choose the appropriate 
ensemble for your MD, i.e. what is to be held constant. Different programs 
will often have different ensembles implemented, so you may be forced to 
use a particular program in order to model your system. In CASTEP the 
number of particles is always kept constant, but you need to choose 
whether to have constant volume or pressure, and whether to have constant 
energy or temperature -- in other words NVE, NVT, NPH or NPT.

Of course if your favourite program doesn't have the ensemble you need, 
you may be able to persuade the developers to add it -- I'd certainly be 
happy to discuss adding anything to CASTEP if it was important to your 
work.

Accurate ab initio MD typically requires time steps of the order of 1fs 
(possibly even less for low mass nuclei). Each time step is an ab initio 
calculation, and hence time consuming, so you will probably be limited to 
total simulation times of 5-10ps -- depending of course on your simulation 
cell, the computing power you have available, and how much patience you 
have! In any case you should make sure that the physics or chemistry 
you're interested in will be well sampled by a molecular dynamics run of 
this length, or you could end up wasting a lot of time.

Depending on the molecule you're interested in, quantum nuclear effects 
might also be important in which case you might like to investigate 
path-integral MD. This is typically most important for low-mass nuclei 
and/or highly anisotropic energy landscapes.

I hope that's been helpful, I'm not sure I can add much more without 
knowing more details about your calculation. If you are happy to post more 
information (on CCL or direct to me), I might be able to offer more 
specific advice.

Yours,

Phil Hasnip
(a CASTEP developer)

-------------------------------------------------------
Dr Phil Hasnip            Email: phil.hasnip^^york.ac.uk
Dept of Physics
University of York        Tel:  +44 (0)1904 324624
York YO10 5DD


From owner-chemistry@ccl.net Wed Dec  7 08:33:00 2011
From: "bonoit bonoit bonoit_10..yahoo.fr" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: PCM model
Message-Id: <-46007-111207080209-18073-j8kt1egSn+HN11jh5UgsEw###server.ccl.net>
X-Original-From: "bonoit  bonoit" <bonoit_10+*+yahoo.fr>
Date: Wed, 7 Dec 2011 08:02:08 -0500


Sent to CCL by: "bonoit  bonoit" [bonoit_10\a/yahoo.fr]
Dear CCLers,
I have a small question about PCM Model;
How to calculate non-electrostatic terms for PCM model?
Thank you in advance
Sincerely,
Bonoit


From owner-chemistry@ccl.net Wed Dec  7 09:08:00 2011
From: "bonoit bonoit bonoit_10[-]yahoo.fr" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Orbital overlap S
Message-Id: <-46008-111207082326-4019-ojukA5bhWNi+ADWeuLvmUw{:}server.ccl.net>
X-Original-From: "bonoit  bonoit" <bonoit_10~!~yahoo.fr>
Date: Wed, 7 Dec 2011 08:23:25 -0500


Sent to CCL by: "bonoit  bonoit" [bonoit_10]*[yahoo.fr]
Dear CCLers,

What are the integrals that are monoelectronic and those which are bielectronic in the Hartree-Fock method?
For exemple: Srs it's mono or bielectronic?

My second question is about the chemical bond, is it formed by electrons or by orbital overlap or by the combination of these two elements?

Thank you in advance
Sincerely,
BOnoit


From owner-chemistry@ccl.net Wed Dec  7 10:08:00 2011
From: "Ian Grant Ian.Grant..ruhr-uni-bochum.de" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: citation style
Message-Id: <-46009-111207091336-27945-g4o7he2DueXu++LGDBCL2w-.-server.ccl.net>
X-Original-From: "Ian Grant" <Ian.Grant . ruhr-uni-bochum.de>
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Date: 7 Dec 2011 15:13:25 +0100
MIME-Version: 1.0


Sent to CCL by: "Ian Grant" [Ian.Grant[A]ruhr-uni-bochum.de]
This is a multi-part message in MIME format.
--------------030207040206080900020406
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Mendeley uses Citation Style Language (CSL), just like Zotero. You can 
see if there is already a style for the journal you require in the 
Zotero Style Repository: http://www.zotero.org/styles

People also create styles, put them in the GitHub for Zotero and share 
them by posting to the Zotero forums. Hence you could also try looking 
there ( http://forums.zotero.org/11/), as somebody might have created 
the style you want but it hasn't made it to the official repository 
above (I say this because I shared one I created in May via the forums 
but it's not in the repository yet).

Unfortunately I don't think there is an existing style that suits your 
needs (I searched for 'molecular structure' and found nothing), so you 
have two options:

1. Request a style, and a helpful (Zotero) user might create it for you: 
https://github.com/citation-style-language/styles/wiki/Requesting-Styles

2. Create the style yourself. It's best to take an existing, 
closely-related CSL file and adjust it to your needs. You can find 
useful information here: 
https://github.com/citation-style-language/styles/wiki/Editing-Styles 
and an example, step-by-step guide here: 
http://www.zotero.org/support/dev/citation_styles/style_editing_step-by-step
If you do create a style, don't forget to give it back to the community 
for that warm, fuzzy feeling!

Hope that helps.


P.S. FWIW, I seem to recall there once was an .ens to .csl converter 
developed by the Zotero crew, but it was swiftly buried when 
Thomson-Reuters (EndNote) sued George Mason U (Zotero) because of this 
very feature.



On 06/12/11 21:32, ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com wrote:
> Dear CCL members,
>
>       This question regards to citation style. I'm about to finish a 
> paper for a journal (Journal of Molecular structure:theochem).As you 
> know it is painful to write 50 or more references manually and manage 
> them. I am mendeley user but this citation style is not there in 
> mendeley repo ( use .csl extension). I have the citation style for 
> Endnote (.ens extension). So need a help to write my citation in above 
> journal format. Please suggest the easiest way. Is there  any way to 
> convert the .ens to .csl or any valuable suggestion from your side. I 
> will be grateful to you. Thank you.
>
>
>
> ****************************************************
>
> *ABHISHEK SHAHI*
>
> /Research Scholar
> Inorganic and Physical Chemistry
> Indian Institute Of Science
> Bangalore-12/
> E-mail: shahi]~[ipc.iisc.ernet.in <mailto:shahi]%7E[ipc.iisc.ernet.in>
> shahi.abhishek1984]~[gmail.com <mailto:shahi.abhishek1984]%7E[gmail.com>
> *
> *
> *****************************************************
>

-- 

<http://www.ruhr-uni-bochum.de/>
------------------------------------------------------------------------
Ian M. Grant MSci, PhD (Bris) [ian.grant]~[ruhr-uni-bochum.de]
Centre for Theoretical Chemistry <http://www.theochem.ruhr-uni-bochum.de>
Ruhr-Universität Bochum <http://www.ruhr-uni-bochum.de/>
44780 Bochum, Germany
Office: NC 03/51 <http://bit.ly/map-rub-nc> --- Tel.: +49 234 32 26751

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<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    Mendeley uses Citation Style Language (CSL), just like Zotero. You
    can see if there is already a style for the journal you require in
    the Zotero Style Repository:
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
    <a href="http://www.zotero.org/styles">http://www.zotero.org/styles</a><br>
    <br>
    People also create styles, put them in the GitHub for Zotero and
    share them by posting to the Zotero forums. Hence you could also try
    looking there (
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
    <a href="http://forums.zotero.org/11/">http://forums.zotero.org/11/</a>),
    as somebody might have created the style you want but it hasn't made
    it to the official repository above (I say this because I shared one
    I created in May via the forums but it's not in the repository yet).<br>
    <br>
    Unfortunately I don't think there is an existing style that suits
    your needs (I searched for 'molecular structure' and found nothing),
    so you have two options:<br>
    <br>
    1. Request a style, and a helpful (Zotero) user might create it for
    you:
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
    <a
href="https://github.com/citation-style-language/styles/wiki/Requesting-Styles">https://github.com/citation-style-language/styles/wiki/Requesting-Styles</a><br>
    <br>
    2. Create the style yourself. It's best to take an existing,
    closely-related CSL file and adjust it to your needs. You can find
    useful information here:
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
    <a
href="https://github.com/citation-style-language/styles/wiki/Editing-Styles">https://github.com/citation-style-language/styles/wiki/Editing-Styles</a>
    and an example, step-by-step guide here:
    <meta http-equiv="content-type" content="text/html;
      charset=ISO-8859-1">
    <a
href="http://www.zotero.org/support/dev/citation_styles/style_editing_step-by-step">http://www.zotero.org/support/dev/citation_styles/style_editing_step-by-step</a><br>
    If you do create a style, don't forget to give it back to the
    community for that warm, fuzzy feeling!<br>
    <br>
    Hope that helps.<br>
    <br>
    <br>
    P.S. FWIW, I seem to recall there once was an .ens to .csl converter
    developed by the Zotero crew, but it was swiftly buried when
    Thomson-Reuters (EndNote) sued George Mason U (Zotero) because of
    this very feature.<br>
    <br>
    <br>
    <br>
    On 06/12/11 21:32, ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com
    wrote:
    <blockquote
cite="mid:-id%235yt-45999-111206153234-708-ZTztjF0l9bAggqqyWpRaCQ]~[server.ccl.net"
      type="cite">Dear CCL members,&nbsp;
      <div><br>
      </div>
      <div>&nbsp; &nbsp; &nbsp; This question regards to citation style. I'm about to
        finish a paper for a journal (Journal of
        Molecular&nbsp;structure:theochem).As you know it is painful to write
        50 or more references&nbsp;manually and manage them. I am mendeley
        user but this citation style is not there in mendeley repo ( use
        .csl extension). I have the citation style&nbsp;for Endnote (.ens
        extension). So need a help to write my citation in above
        journal&nbsp;format. Please suggest the easiest way. Is there &nbsp;any
        way to convert the .ens to .csl or any valuable suggestion from
        your side. I will be&nbsp;grateful&nbsp;to you. Thank you.</div>
      <div><br>
      </div>
      <div><br>
        <span style="font-family:times new roman,serif"><br>
          <font color="#ff0000">****************************************************</font><br>
        </span><br>
        <span style="background-color:rgb(255, 255, 255)">&nbsp;<font
            style="font-family:trebuchet ms,sans-serif" size="4"><b><span
                style="color:rgb(51, 51, 255)">ABHISHEK SHAHI</span></b></font></span><br>
        <br>
        <i style="font-family:courier new,monospace"><span
            style="background-color:rgb(255, 255, 255);color:rgb(0, 102,
            0)">Research Scholar</span><br
            style="background-color:rgb(255, 255, 255);color:rgb(0, 102,
            0)">
          <span style="background-color:rgb(255, 255, 255);color:rgb(0,
            102, 0)">Inorganic and Physical Chemistry</span><br
            style="background-color:rgb(255, 255, 255);color:rgb(0, 102,
            0)">
          <span style="background-color:rgb(255, 255, 255);color:rgb(0,
            102, 0)">Indian Institute Of Science</span><br
            style="background-color:rgb(255, 255, 255);color:rgb(0, 102,
            0)">
          <span style="background-color:rgb(255, 255, 255);color:rgb(0,
            102, 0)">Bangalore-12</span></i> <br>
        <span style="font-family:arial black,sans-serif"><span
            style="color:rgb(255, 0, 0)">E-mail:</span> &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
        </span><a moz-do-not-send="true" style="font-family:arial
          black,sans-serif" href="mailto:shahi]%7E[ipc.iisc.ernet.in"
          target="_blank">shahi]~[ipc.iisc.ernet.in</a><br
          style="font-family:arial black,sans-serif">
        <span style="font-family:arial black,sans-serif">&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><a moz-do-not-send="true"
          style="font-family:arial black,sans-serif"
          href="mailto:shahi.abhishek1984]%7E[gmail.com" target="_blank">shahi.abhishek1984]~[gmail.com</a><br>
        <b style="font-family:arial black,sans-serif"><br
            style="color:rgb(255, 0, 0)">
        </b><span style="font-family:times new roman,serif"><font
            class="Apple-style-span" color="#ff0000"><br>
          </font>
          <font color="#ff0000">*****************************************************</font></span><br>
        <br>
      </div>
    </blockquote>
    <br>
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      <a href="http://www.ruhr-uni-bochum.de/" style="text-decoration:
        none !important; float: left;">
        <svg xmlns:svg="http://www.w3.org/2000/svg"
          xmlns="http://www.w3.org/2000/svg" version="1.0" width="0"
          height="0" id="svg2443" xml:space="preserve" viewBox="0 0 90
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                    style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:none"></path></g><g
                  transform="translate(42.3223,22.3027)" id="g2472"><path
                    d="M 0,0 C 4.05,2.297 5.61,5.711 5.61,9.164 C
                    5.61,14.852 1.543,19.283 -4.469,19.283 L
                    -17.287,19.283 L -17.287,-9.688 L -10.989,-9.688 L
                    -10.989,14.164 L -6.036,14.164 C -2.508,14.164
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                    -2.086,4.144 -5.995,4.144 L -9.96,4.144 L 0,-9.688 L
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                    style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:none"></path></g></g></g></g></svg>
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        helvetica, sans-serif !important; font-size: 1.0em; line-height:
        1.2em; ">
        <div> <span style="font-weight: bold;">Ian M. Grant</span>&nbsp; <span
            style="font-family: RubFlama Light, Metrophobic, helvetica,
            sans-serif; font-size: 90%; padding-left: 0.55em;">MSci, PhD
            (Bris)</span>&nbsp; <span style="font-style: italic;
            font-family: RubFlama Light, helvetica, sans-serif;
            padding-left: 0.6em; font-size: 86%;">[<a class="moz-txt-link-abbreviated" href="mailto:ian.grant]~[ruhr-uni-bochum.de">ian.grant]~[ruhr-uni-bochum.de</a>]</span>
          <br>
          <a href="http://www.theochem.ruhr-uni-bochum.de"
            style="text-decoration: none; color: inherit;">Centre for
            Theoretical Chemistry</a> <br>
          <a href="http://www.ruhr-uni-bochum.de/"
            style="text-decoration: none; color: inherit;">Ruhr-Universit&auml;t
            Bochum</a> <br>
          44780 Bochum, Germany <br>
          Office: <a id="map" href="http://bit.ly/map-rub-nc"
            style="text-decoration: none !important; color: inherit;
            border-bottom: 2px dotted #e6e4e4;" title="Map: location of
            building NC on the RUB campus">NC 03/51</a> &#8212; Tel.: +49 234
          32 26751 <br>
        </div>
      </div>
    </div>
  </body>
</html>

--------------030207040206080900020406--


From owner-chemistry@ccl.net Wed Dec  7 10:42:00 2011
From: "Iain Moal Iain.Moal^^^cancer.org.uk" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: citation style
Message-Id: <-46010-111207104050-22561-kVTSkRPlC6H7AxR9lDtQ8Q^-^server.ccl.net>
X-Original-From: Iain Moal <Iain.Moal,+,cancer.org.uk>
Content-Language: en-GB
Content-Transfer-Encoding: 8bit
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Date: Wed, 7 Dec 2011 15:40:21 +0000
MIME-Version: 1.0


Sent to CCL by: Iain Moal [Iain.Moal%a%cancer.org.uk]
Bibtex is certainly not just for LaTeX. When I want to use my bibtex library in a word document I use the bibtex4word add-in, which does exactly what I want. I use JabRef for managing the references and if a style is not available, I use the custom-bib package to generate my own style with the precise layout I need. I can't compare with EndNote or Mendeley, as I have never used them. I have never felt the need.

Iain Moal

________________________________________
> From: owner-chemistry+iain.moal==cancer.org.uk*o*ccl.net [owner-chemistry+iain.moal==cancer.org.uk*o*ccl.net] On Behalf Of Sebastian Kozuch kozuchs]*[yahoo.com [owner-chemistry*o*ccl.net]
Sent: 07 December 2011 12:21
To: Iain Moal
Subject: CCL: citation style

Sent to CCL by: Sebastian Kozuch [kozuchs###yahoo.com]


I know it's not a computational chemistry topic, but it is a matter of everyday use for all scientists. So I'm interested to know the opinion of people with experience on reference software.
I don't have Endnote, and I will not pay for it. However, I made a pact with the devil, so I use Windows and Word.
I use Zotero for references, which is free but has a couple of issues, most important one is that it works only inside firefox (not a problem for me). I am happy with it. Once I didn't have the reference format of one particular journal, but I managed to build it based on another similar style.

Endnote web is for free, but last time I tried it was quite useless. Bibtex is for latex, and I will not learn latex. Period. (It is not my intention to start a public debate on latex vs. word).

What about Mendeley? Did someone tried Qiqqa? Another option that comes to your mind?


Best,

Sebastian Kozuch



________________________________
> From: Michel Petitjean petitjean.chiral(-)gmail.com <owner-chemistry[#]ccl.net>
To: "Kozuch, Sebastian " <kozuchs[#]yahoo.com>
Sent: Wednesday, December 7, 2011 10:18 AM
Subject: CCL: citation style


Sent to CCL by: Michel Petitjean [petitjean.chiral=-=gmail.com]
Dear Abhishek,
Bannish Word, Endnote, etc. Most of your problems will be solved with
using latex, bibtex.
Also, bannish Windows PCs. Use linux, or eventually macosx.
Sincerely,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral _ gmail.com (preferred),
michel.petitjean _ univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2011/12/6 ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com
<owner-chemistry _ ccl.net>:
> Dear CCL members,
>
>       This question regards to citation style. I'm about to finish a paper
> for a journal (Journal of Molecular structure:theochem).As you know it is
> painful to write 50 or more references manually and manage them. I am
> mendeley user but this citation style is not there in mendeley repo ( use
> .csl extension). I have the citation style for Endnote (.ens extension). So
> need a help to write my citation in above journal format. Please suggest the
> easiest way. Is there  any way to convert the .ens to .csl or any valuable
> suggestion from your side. I will be grateful to you. Thank you.
>
>
>
> ****************************************************
>
>  ABHISHEK SHAHI
>
> Research Scholar
> Inorganic and Physical Chemistry
> Indian Institute Of Science
> Bangalore-12
> E-mail:                  shahi]~[ipc.iisc.ernet.in
>                                 shahi.abhishek1984]~[gmail.com
>
>
> *****************************************************http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Wed Dec  7 11:30:00 2011
From: "Adam Tenderholt atenderholt]![gmail.com" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: citation style
Message-Id: <-46011-111207112716-10765-iuhTQn2FpfQCL0g+OMqxjw _ server.ccl.net>
X-Original-From: Adam Tenderholt <atenderholt..gmail.com>
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Date: Wed, 7 Dec 2011 08:27:08 -0800
MIME-Version: 1.0


Sent to CCL by: Adam Tenderholt [atenderholt{=}gmail.com]
Since a few people have mentioned LaTeX/BibTex, I'll follow up by
suggesting you look at LyX. It's a Free, cross-platform front-end to
LaTeX that tries to behave like a standard WYSIWYG program like MS
Word. I've used it for a couple of manuscripts, and while it has its
share of quirks, I find it much better than Word for long documents
with multiple figures and citations.

Adam


On Wed, Dec 7, 2011 at 1:43 AM, Vincent Leroux
vincent.leroux*_*loria.fr <owner-chemistry{}ccl.net> wrote:
>
> Sent to CCL by: Vincent Leroux [vincent.leroux[*]loria.fr]
>
> Well, there is an easy solution. Select all the citations you wish to use
> from Mendeley, and export them as "Endnote XML". Then import the resulting
> XML file into EndNote, and use it as usual. This works the other way, too.
>
> Note: you may consider dropping out EndNote and Word, as Michel suggested,
> because these programs are instruments of torture, but going for
> BibTex/LaTeX/Linux at the present time may also be going straight to hell
> with good intents. I am especially thinking of the situation where you are
> working with colleagues on a paper: you may not be very popular if you try
> to enforce using LaTeX to others, and you will probably end up doing more
> work than needed if as the main author you stick yourself to it while others
> keep using what they are used to (and they will!). Good news for you: more
> citation styles and better integration with Word/OpenOffice/etc. is one of
> the current development priorities for Mendeley. We may eventually be able
> to trash EndNote for good soon... (next shall be Word! one step at a
> time...)
>
>
>
> On 06/12/2011 21:32, ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com wrote:
>>
>> Dear CCL members,
>>
>>       This question regards to citation style. I'm about to finish a
>> paper for a journal (Journal of Molecular structure:theochem).As you
>> know it is painful to write 50 or more references manually and manage
>> them. I am mendeley user but this citation style is not there in
>> mendeley repo ( use .csl extension). I have the citation style for
>> Endnote (.ens extension). So need a help to write my citation in above
>> journal format. Please suggest the easiest way. Is there  any way to
>> convert the .ens to .csl or any valuable suggestion from your side. I
>> will be grateful to you. Thank you.
>>
>>
>>
>> ****************************************************
>>
>> *ABHISHEK SHAHI*
>>
>> /Research Scholar
>>
>> Inorganic and Physical Chemistry
>> Indian Institute Of Science
>> Bangalore-12/
>> E-mail: shahi]~[ipc.iisc.ernet.in <mailto:shahi]~[ipc.iisc.ernet.in>
>> shahi.abhishek1984]~[gmail.com <mailto:shahi.abhishek1984]~[gmail.com>
>> *
>> *
>> *****************************************************>    >         http://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>    >
>


From owner-chemistry@ccl.net Wed Dec  7 22:34:01 2011
From: "=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?= kacper.druzbicki=-=uj.edu.pl" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: wb97XD in g09
Message-Id: <-46012-111207223146-24848-bHKOgb5KkySlL43BIev/Cw~!~server.ccl.net>
X-Original-From: =?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?= <kacper.druzbicki%uj.edu.pl>
Content-disposition: inline
Content-language: pl
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=iso-8859-2
Date: Thu, 08 Dec 2011 04:31:37 +0100
MIME-version: 1.0


Sent to CCL by: =?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?= [kacper.druzbicki_._uj.edu.pl]
Hello,

I don't know what was the reason of using wB97XD in your case. I just want to say that if you need to contribute some dispersion into your calculations you can also use the empirical Grimme's corrections in the new revisions of G09. Probably it's not an answer to your question, but it may be worth to be mentioned, since you could also try some other functionals. 

For the empirical dispersion term, the s6 scaling factor depends on the type of functional used, so it is necessary to calibrate the amount of the correction to add depending on the functional. There is only a limited number of functionals for which s6 scale factors had been derived. In G09, the default is to add the empirical dispersion term only for the functionals for which there is a keyword to invoke the model that includes such term. These keywords are:

B97D        S6 = 1.25
B2PLYPD     S6 = 0.55
mPW2PLYPD   S6 = 0.40
wB97XD      S6 = 1.00 (D = 6.00)

Just by using any of these keywords, you would be doing a calculation using the requested functional plus the corresponding empirical dispersion term. If you have G09 rev. B.01 or the newest version C.01, there are a few other functionals for which s6 scale factors were also proposed but there is not a keyword to invoke the model that includes the empirical dispersion term. These functionals are:

PBEPBE      S6 = 0.75
BLYP        S6 = 1.2
B3LYP       S6 = 1.05
BP86        S6 = 1.05
TPSSTPSS    S6 = 1.0

In order to use any of the above listed functionals including an empirical dispersion term with the corresponding s6 scale factor, you would need to use the the keyword of the functional an also add "IOp(3/124=3)". This won't work on G09 rev. A, where it would use s6 = 1 only.

Good Luck,
Casper

Kacper Dru¿bicki,
Faculty of Chemistry,
Department of Chemical Physics,
Jagiellonian University,
Ingardena Street 3, 30-060 Cracow, Poland
phone: +48 12 6632265

----- Wiadomo¶æ oryginalna -----
Od: "quartarolo|a|unical.it" <owner-chemistry-x-ccl.net>
Data: Czwartek, Grudzieñ 1, 2011 1:44 pm
Temat: CCL:G: wb97XD in g09
Do: "Druzbicki, Kacper " <kacper.druzbicki-x-uj.edu.pl>


> Sent to CCL by: quartarolo _ unical.it
> Dear all,
> I'm running a calculation with Gaussian09 for a Lutetium complex using 
>  
> the wB97XD functional.
> The program stops with the following message:
> "R6DR0: No vdW radius available for IA= 71".
> Is there a way to define this parameter manually in the input file and 
>  
> eventually where to search for vdW radius of lutetium.
> 
> best regards
> 
> Quartarolo Domenico
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> 
> 
> 
> 
> 
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