From owner-chemistry@ccl.net Sun Feb 21 01:23:01 2010
From: ",,yahoo.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL:G: G03 Temperature Parameter
Message-Id: <-41296-100221012140-14549-guteVaMOawWJie7H0rW++g%%server.ccl.net>
X-Original-From: <a/yahoo.com>
Content-Type: multipart/alternative; boundary="0-10499551-1266733288=:86886"
Date: Sat, 20 Feb 2010 22:21:28 -0800 (PST)
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Sent to CCL by: ===yahoo.com]
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Dear All,
I would like to know how I can enter the environment temperature in my computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any other software you recommend.

Thank you in advance.
Best regards,
A.F



      
--0-10499551-1266733288=:86886
Content-Type: text/html; charset=us-ascii

<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear All,<br>I would like to know how I can enter the environment temperature in my computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any other software you recommend.<br><br>Thank you in advance.<br>Best regards,<br>A.F<br></td></tr></table><br>

      
--0-10499551-1266733288=:86886--


From owner-chemistry@ccl.net Sun Feb 21 06:02:00 2010
From: "Alex Naden anaden{=}fsmail.net" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Estimation of viscosity from molecular weight
Message-Id: <-41297-100221055915-17241-9whWpCCMagMLNHD/2rmRyQ^_^server.ccl.net>
X-Original-From: "Alex  Naden" <anaden-#-fsmail.net>
Date: Sun, 21 Feb 2010 05:59:11 -0500


Sent to CCL by: "Alex  Naden" [anaden{:}fsmail.net]
Hi guys,

I am not sure where my question is going but it somehow does not look like a right direction... I need to explain the differences in a diffusion zone of some liquids on a solid surface, so my first idea was to look at the differences in their viscosities. As the only data that I have for the compounds was the molecular weight and their structure my idea was to estimate viscosities (if possible). If there are any useful suggestions on the subject they will be VERY welcome.

Thank you,

Alex


From owner-chemistry@ccl.net Sun Feb 21 09:14:00 2010
From: "Matthew Tassell mtassell!=!gmail.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL:G: True energy of transition state
Message-Id: <-41298-100221091209-8843-DkToLcB/I+VVYZFo9dqjsA^^server.ccl.net>
X-Original-From: "Matthew   Tassell" <mtassell/a\gmail.com>
Date: Sun, 21 Feb 2010 09:12:05 -0500


Sent to CCL by: "Matthew   Tassell" [mtassell(-)gmail.com]
Dear CCL

I have recently been trying to calculate the barrier heights for a reaction between a aldehyde radical and double bond. 

When i look at the thermochemistry data for the transition state i'm not entirly sure how to go about taking into consideration various corrections, zero-point etc.

I have searched the CCl site, internet and read the gaussian thermochemistry white paper but still not sure how to go about finding the answer.

If anybody has experience in these matters and could point me in the right direction i would be very grateful.

Many thanks in advance


From owner-chemistry@ccl.net Sun Feb 21 12:02:00 2010
From: "Wolf-D. Ihlenfeldt wdi/./xemistry.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: AW: can you recommend software to compare chemical databases and exclude duplicates pls
Message-Id: <-41299-100221065920-12530-KPPi6HPLg9IjMnTD0WXSQQ||server.ccl.net>
X-Original-From: "Wolf-D. Ihlenfeldt" <wdi]=[xemistry.com>
Content-Language: de
Content-Transfer-Encoding: quoted-printable
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	charset="iso-8859-1"
Date: Sun, 21 Feb 2010 12:59:02 +0100
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Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi[#]xemistry.com]

Ahem - IMHO the outline below is really *NOT* a viable solution.=20

Relying on the ability to decode InChI strings back into a graph is an
unsuitable approach. InChI was not designed for this. The current
implementations of inverters fail on a significant number of strings, =
and on
others the results are often pretty weird tautomers if you have mobile =
H.=20

Also, last I checked OpenBabel did not generate 2D representations - an
regenerated SD file will have all-0 atomic coordinates, which can be a
problem later. And OpenBabel has in general a lot of problems with
stereochemistry - if you need stereochemistry in your project, my =
personal
advice is to stay away from it.


software to compare chemical databases
> and exclude duplicates pls
>=20
>=20
> Sent to CCL by: Vincent Leroux [vincent.leroux+*+loria.fr]
>=20
> Hi Andrew,
>=20
> There is ScreeningAssistant for such a task, and much more.
> http://hal.archives-
> =
ouvertes.fr/docs/00/07/97/12/PDF/monge_Molecular_Diversity_revised_2.pd
> f
> http://dx.doi.org/10.1007/s11030-006-9033-5
> http://dx.doi.org/10.2174/157340908785747410
>=20
> SA is really boxing in the heavyweight category of chemoinformatics
> tools so you might prefer to process data by yourself.
> My suggestions :
>=20
> - first "clean up" db1.sdf and db2.sdf: remove salts, hydrogens etc.
> everything in the structure that might differ artificially from one
> supplier to the other. (Open)Babel should do a good job here.
>=20
> - name all molecules in db1.sdf and db2.sdf using scripts. The name
> must
> be on the 1st line in each molecule record and should not contain
> spaces. You want a combination of the supplier name and the molecule
> supplier's unique ID (already in place if you are lucky, else found in
> some MDL tag). Make sure the name does not contain spaces, and that is
> is put in the correct position (1st line).
>=20
> - use the InChI software for generating db1.inchi and db2.inchi, and
> make sure you get text files with 1 line per molecule formatted like:
> <Molecule name> <InChi code>
>=20
> - If the molecules are named Supplier1/<Supplier 1 ID> and
> Supplier2/<Supplier 2 ID> , then use the following commands (have not
> tested them, but should work)
>=20
> cat db[12].inchi | sort -k2 | uniq -s 1 - | grep '^Supplier1/' >
> db1_unique.inchi
> cat db[12].inchi | sort -k2 | uniq -s 1 - | grep '^Supplier2/' >
> db2_unique.inchi
> cat db[12].inchi | sort -k2 | uniq -d -s 1 - | awk '{l=3D$1; getline;
> print l"_aka_"$0}' > db12_common.inchi
>=20
> This will generate db1_unique.inchi, db2_unique.inchi and
> db12_common.inchi - self-explanatory.
>=20
> - use OpenBabel (or equivalent software) for converting your InChI
> files
> to SDF format/2D representation, then Corina (or equivalent) if you
> want
> 3D coordinates, e.g. for docking.
>=20
> Regards,
> VL
>=20
>=20
>=20
> Le 19/02/10 18:45, Andrew Voronkov drugdesign:yandex.ru a =E9crit :
> >
> > Sent to CCL by: Andrew Voronkov [drugdesign%yandex.ru]
> > Dear CCL users,
> > can you please recommend me academics free software or scripts (or
> software with good evaluation period) for comparison of databases. For
> example I want to download two publically available databases and =
unite
> them excluding duplicates into a separate database. So in this case  I
> ll get  one united database  and one database where duplicate =
compounds
> will be (but not duplicated). Can you please suggest such software?
> >
> > Sincerely yours,
> > Andrew
> >
> >
>=20


From owner-chemistry@ccl.net Sun Feb 21 12:37:00 2010
From: "Rohun Chowdhury rohunc.chem*|*gmail.com" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: need info
Message-Id: <-41300-100221085405-7397-IAgnd2A2Q0yBfuQHGnanKQ[-]server.ccl.net>
X-Original-From: "Rohun   Chowdhury" <rohunc.chem{:}gmail.com>
Date: Sun, 21 Feb 2010 08:54:02 -0500


Sent to CCL by: "Rohun   Chowdhury" [rohunc.chem[]gmail.com]
Dear All,
 I want to know how can I determine % of ligand and metal in any particular HOMO or LUMO of my metal complex? Is there any software available for it? Or is there any mathematical procedure by which I can determine above manually 
> from data of my *.log file (obtained from SP calculation using POP(FULL) on optimized geometry)? 

Please help me in that regard. I am very new to this field.

Many thanks in advance.

Rohun


From owner-chemistry@ccl.net Sun Feb 21 13:12:00 2010
From: "Alexander Bagatur yants bagaturyants|-|gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: G03 Temperature Parameter
Message-Id: <-41301-100221030508-19571-g5ekSJORNpPB41zw5oZ2EA]_[server.ccl.net>
X-Original-From: "Alexander Bagatur'yants" <bagaturyants|-|gmail.com>
Content-Language: ru
Content-Transfer-Encoding: 7bit
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	charset="us-ascii"
Date: Sun, 21 Feb 2010 10:05:58 +0300
MIME-Version: 1.0


Sent to CCL by: "Alexander Bagatur'yants" [bagaturyants-*-gmail.com]
Dear All,
I believe that letters should be somehow filtered before posting in the list
or some stricter rules should be established.
Too much garbage has been appearing  in our list recently.
As to this question, I would first recommend the addressee to learn quantum
chemistry or at least physical chemistry before starting work with quantum
chemistry.

Best regards,

Prof. Alexander A. Bagatur'yants
Photochemistry Center
Russian Academy of Sciences
ul. Novatorov 7a
Moscow 119421 Russia
Phone:  +7(495)9362588 (office)
                 +7(916)5317022 (mobile)
Fax:         +7(495)9361255
e-mail: sasha:-:photonics.ru
               bagaturyants:-:gmail.com

> From: owner-chemistry+sasha==photonics.ru:-:ccl.net
[mailto:owner-chemistry+sasha==photonics.ru:-:ccl.net] On Behalf Of,,yahoo.com
Sent: Sunday, February 21, 2010 9:21 AM
To: Bagaturyants, Alexander A. 
Subject: CCL:G: G03 Temperature Parameter

Dear All,
I would like to know how I can enter the environment temperature in my
computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any
other software you recommend.

Thank you in advance.
Best regards,
A.F


From owner-chemistry@ccl.net Sun Feb 21 13:47:01 2010
From: "Mahmoud A. A. Ibrahim m.ibrahim||compchem.net" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: Long time Geometry optimization
Message-Id: <-41302-100221114333-13868-nZPh83krMJWY1PEv6XWyNQ=server.ccl.net>
X-Original-From: "Mahmoud A. A. Ibrahim" <m.ibrahim|compchem.net>
Content-Type: multipart/alternative; boundary=0016e6dab0cdab370d04801f03eb
Date: Sun, 21 Feb 2010 16:43:20 +0000
MIME-Version: 1.0


Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim|*|compchem.net]
--0016e6dab0cdab370d04801f03eb
Content-Type: text/plain; charset=ISO-8859-1

Dear C.C.G.
Time taken for your job depends on the size of your molecules (in addition
to other parameters, like method, basis set, atom types, Computational
facility, starting structure..etc.)
For your system, I think it may take that long time.You are using a large
basis set and doing *Freq *job. I recommend to stop your job and restart it
using guess=read and geom=checkpoint.
Please, bear in your mind the scaling factor for
the thermodynamic parameters. You have to consulate references to see if
there is a scaling factor for your model chemistry before you start, there
are missing scaling factors for some models upto day.
If I were you I would start my calculation using B3LYP/6-31G* (in addition
it is available for Cu). Then you would restart your job using larger basis
set, if you liked. But, I believe *personally*, it will be enough. Many
references prove optimization with level higher than B3LYP/6-31G* doesn't
make any significant difference in results (You should check if it is liable
for Cu too).
I recommend "Exploring chemistry with electronic structure methods" Chapter
4 as a start point.
Sincerely;
M. Ibrahim

On Sat, Feb 20, 2010 at 10:25 PM, CompChem Group CompChemGroup1_+_gmail.com
<owner-chemistry]-[ccl.net> wrote:

>
> Sent to CCL by: "CompChem  Group" [CompChemGroup1-.-gmail.com]
> Dear All,
> Currently, I preform geometry optimization of Dinuclear metal complex (two
> Cu atoms + 100 of H, C, N and O atoms)in order to calculate thermodynamic
> parameters. I use B3LYP/mixed basis set; 6-311g(d,p)for H, C, N and O atoms
> and LANL2DZ for Cu. I use 8 cores for this job. This job consumed long time;
> about 20 days and not finished so far. I have two questions:
>
> 1- Is normal for such job to take this long time?
> 2- Is this basis set is good to calculate the thermodynamic parameters?
> 3- Is there a model chemistry or a method work well but with little time?
>
> By the way the H-atoms are not important, so I can use 6-311g without
> polarization functions.
>
> Your suggestion would be appreciated
> Thanks in advance,
> C.C.G>
>
>


-- 
                 Mahmoud A. A. Ibrahim
                      Current Address
                7.05, School of Chemistry,
             The University of Manchester,
        Oxford Road, Manchester, M13 9PL,
                      United Kingdom.

                       Home Address
                 Chemistry Department,
                    Faculty of Science,
                       Minia University,
                          Minia 61519,
                               Egypt.

                    Contact Information
          Email: m.ibrahim]-[compchem.net
             Website: www.compchem.net
                  Fax No.: +20862342601

--0016e6dab0cdab370d04801f03eb
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear C.C.G.<div>Time taken for your job depends on the size of your molecul=
es (in addition to other parameters, like method, basis set, atom types, Co=
mputational facility, starting structure..etc.)</div><div>For your system, =
I think it may take that long time.You are using a large basis set and doin=
g <b>Freq </b>job. I recommend to stop your job and restart it using guess=
=3Dread and geom=3Dcheckpoint.=A0</div>
<div>Please, bear in your mind the=A0scaling=A0factor for the=A0thermodynam=
ic=A0parameters. You have to consulate references to see if there is a=A0sc=
aling=A0factor for your model chemistry before you start, there are missing=
=A0scaling=A0factors for some models upto day.</div>
<div>If I were you I would start my calculation using B3LYP/6-31G* (in addi=
tion it is available for Cu). Then you would restart your job using larger =
basis set, if you liked. But, I believe <b>personally</b>, it will be=A0eno=
ugh. Many references prove optimization with level higher than B3LYP/6-31G*=
=A0doesn&#39;t make any significant difference in results (You should check=
 if it is liable for Cu too).=A0</div>
<div>I recommend &quot;Exploring chemistry with electronic structure method=
s&quot; Chapter 4 as a start point.</div><div>Sincerely;</div><div>M. Ibrah=
im<br><br><div class=3D"gmail_quote">On Sat, Feb 20, 2010 at 10:25 PM, Comp=
Chem Group CompChemGroup1_+_<a href=3D"http://gmail.com">gmail.com</a> <spa=
n dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]-[ccl.net">owner-chemistr=
y]-[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>
Sent to CCL by: &quot;CompChem =A0Group&quot; [CompChemGroup1-.-<a href=3D"=
http://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Dear All,<br>
Currently, I preform geometry optimization of Dinuclear metal complex (two =
Cu atoms + 100 of H, C, N and O atoms)in order to calculate thermodynamic p=
arameters. I use B3LYP/mixed basis set; 6-311g(d,p)for H, C, N and O atoms =
and LANL2DZ for Cu. I use 8 cores for this job. This job consumed long time=
; about 20 days and not finished so far. I have two questions:<br>

<br>
1- Is normal for such job to take this long time?<br>
2- Is this basis set is good to calculate the thermodynamic parameters?<br>
3- Is there a model chemistry or a method work well but with little time?<b=
r>
<br>
By the way the H-atoms are not important, so I can use 6-311g without polar=
ization functions.<br>
<br>
Your suggestion would be appreciated<br>
Thanks in advance,<br>
C.C.G<br>
<br>
<br>
<br>
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<br>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br> =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0 <br> =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 7.05, School of Chemistry,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi=
ty of Manchester,<br>
 =A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL, <br> =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.<br><br> =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0Home Address<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
Chemistry Department,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o=
f Science,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers=
ity,<br>
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,<br> =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt. <br><br> =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information<br> =A0 =A0 =A0=
 =A0 =A0 Email: <a href=3D"mailto:m.ibrahim]-[compchem.net">m.ibrahim]-[compche=
m.net</a><br>
 =A0 =A0 =A0 =A0 =A0 =A0 =A0Website: <a href=3D"http://www.compchem.net">ww=
w.compchem.net</a><br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623=
42601<br>
</div>

--0016e6dab0cdab370d04801f03eb--


From owner-chemistry@ccl.net Sun Feb 21 14:21:01 2010
From: "Mahmoud A. A. Ibrahim m.ibrahim-.-compchem.net" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: G03 Temperature Parameter
Message-Id: <-41303-100221120456-16191-Mg8pfjGiQCzjNpv+Rkdt/g,+,server.ccl.net>
X-Original-From: "Mahmoud A. A. Ibrahim" <m.ibrahim---compchem.net>
Content-Type: multipart/alternative; boundary=0016e6db2d231b71db04801f50c9
Date: Sun, 21 Feb 2010 17:04:43 +0000
MIME-Version: 1.0


Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim^compchem.net]
--0016e6db2d231b71db04801f50c9
Content-Type: text/plain; charset=ISO-8859-1

Dear Arash
You can use the following obvious keyword:
Temperature=XXX
where XXX is the desired temperature in Kelvin1
Sincerely;
M. Ibrahim

On Sun, Feb 21, 2010 at 6:21 AM, yahoo.com <
owner-chemistry]~[ccl.net> wrote:

> Dear All,
> I would like to know how I can enter the environment temperature in my
> computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any
> other software you recommend.
>
> Thank you in advance.
> Best regards,
> A.F
>
>


-- 
                 Mahmoud A. A. Ibrahim
                      Current Address
                7.05, School of Chemistry,
             The University of Manchester,
        Oxford Road, Manchester, M13 9PL,
                      United Kingdom.

                       Home Address
                 Chemistry Department,
                    Faculty of Science,
                       Minia University,
                          Minia 61519,
                               Egypt.

                    Contact Information
          Email: m.ibrahim]~[compchem.net
             Website: www.compchem.net
                  Fax No.: +20862342601

--0016e6db2d231b71db04801f50c9
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<span class=3D"Apple-style-span" style=3D"font-family: &#39;Times New Roman=
&#39;; font-size: medium; -webkit-border-horizontal-spacing: 2px; -webkit-b=
order-vertical-spacing: 2px; ">Dear Arash<br>You can use the following obvi=
ous keyword:<br>
Temperature=3DXXX<br>where XXX is the desired temperature in Kelvin1=A0</sp=
an><div><span class=3D"Apple-style-span" style=3D"font-family: &#39;Times N=
ew Roman&#39;; font-size: medium; -webkit-border-horizontal-spacing: 2px; -=
webkit-border-vertical-spacing: 2px; ">Sincerely;=A0<br>
M. Ibrahim<br></span><br><div class=3D"gmail_quote">On Sun, Feb 21, 2010 at=
 6:21 AM, <a href=3D"http://yahoo.com">yahoo.c=
om</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]~[ccl.net">own=
er-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;"><table cellspacing=3D"0" cellpadding=3D"0" =
border=3D"0"><tbody><tr><td valign=3D"top" style=3D"font:inherit">Dear All,=
<br>I would like to know how I can enter the environment temperature in my =
computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any ot=
her software you recommend.<br>
<br>Thank you in advance.<br>Best regards,<br>A.F<br></td></tr></tbody></ta=
ble><br>

      </blockquote></div><br><br clear=3D"all"><br>-- <br> =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0 <br> =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address<br> =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 7.05, School of Chemistry,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0The Univ=
ersity of Manchester,<br>
 =A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL, <br> =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.<br><br> =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0Home Address<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
Chemistry Department,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o=
f Science,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers=
ity,<br>
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,<br> =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt. <br><br> =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information<br> =A0 =A0 =A0=
 =A0 =A0 Email: <a href=3D"mailto:m.ibrahim]~[compchem.net">m.ibrahim]~[compche=
m.net</a><br>
 =A0 =A0 =A0 =A0 =A0 =A0 =A0Website: <a href=3D"http://www.compchem.net">ww=
w.compchem.net</a><br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623=
42601<br>
</div>

--0016e6db2d231b71db04801f50c9--


From owner-chemistry@ccl.net Sun Feb 21 14:58:01 2010
From: "Mahmoud A. A. Ibrahim m.ibrahim%a%compchem.net" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL: Geometry optimization and Single point Scaling
Message-Id: <-41304-100221120803-17526-1GTRAUkkOwXQryg0rSty+Q_-_server.ccl.net>
X-Original-From: "Mahmoud A. A. Ibrahim" <m.ibrahim\a/compchem.net>
Content-Type: multipart/alternative; boundary=0016e6d784e34f83fd04801f4442
Date: Sun, 21 Feb 2010 17:01:25 +0000
MIME-Version: 1.0


Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim#,#compchem.net]
--0016e6d784e34f83fd04801f4442
Content-Type: text/plain; charset=ISO-8859-1

Dear Sayed
What kind of molecular system have you tested?
I am not sure if it is helpful for you but you should know *Small *jobs may
take time in a serial mode shorter than on a parallel one. For example,
molecular mechanics using amber keyword of a *model *of active site of an
enzyme takes around less than of one minute on my PC, while it takes more
than 4 minutes to be accomplished on 4 nodes. Parallel task takes time to
divide and collect data over the nodes.
It means that you should scale the performance on a large system.
Also, bear in your mind there is a difference between real time and CPU
time.
Sincerely;
M. Ibrahim

On Sat, Feb 20, 2010 at 10:56 PM, Sayed Mes Elsayed.elmes(_)yahoo.com <
owner-chemistry-,-ccl.net> wrote:

>
> Sent to CCL by: "Sayed  Mes" [Elsayed.elmes]^[yahoo.com]
> Dear Subscribers,
> I preformed scaling for "Geometry optimization (only 4 steps)" and "Single
> point Scaling" for first row transition metal complex with 1,2,4 and 8 cores
> on MPI cluster. DFT method is used for this purpose. I found that there is
> no difference among them; i.e. the time consuming with 1 core is nearly the
> same like 2 or 4 or 8 cores.
>
> Anybody know why there is no difference in consuming time among them?
>
>  Thanks,
> Sayed>
>
>


-- 
                 Mahmoud A. A. Ibrahim
                      Current Address
                7.05, School of Chemistry,
             The University of Manchester,
        Oxford Road, Manchester, M13 9PL,
                      United Kingdom.

                       Home Address
                 Chemistry Department,
                    Faculty of Science,
                       Minia University,
                          Minia 61519,
                               Egypt.

                    Contact Information
          Email: m.ibrahim-,-compchem.net
             Website: www.compchem.net
                  Fax No.: +20862342601

--0016e6d784e34f83fd04801f4442
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Sayed<div>What kind of molecular system have you tested?</div><div>I a=
m not sure if it is helpful for you but you should know=A0<b>Small </b>jobs=
 may take time in a serial mode shorter than on a parallel one. For example=
, molecular mechanics using amber keyword of a <b>model </b>of active site =
of an enzyme takes around less than of one minute on my PC, while it takes =
more than 4 minutes to be accomplished on 4 nodes. Parallel task takes time=
 to divide and collect data over the nodes.</div>
<div>It means that you should scale the performance on a large system.</div=
><div>Also, bear in your mind there is a difference between real time and C=
PU time.</div><div>Sincerely;</div><div>M. Ibrahim<br><br><div class=3D"gma=
il_quote">
On Sat, Feb 20, 2010 at 10:56 PM, Sayed Mes Elsayed.elmes(_)<a href=3D"http=
://yahoo.com">yahoo.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-c=
hemistry-,-ccl.net">owner-chemistry-,-ccl.net</a>&gt;</span> wrote:<br><blockqu=
ote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc s=
olid;padding-left:1ex;">
<br>
Sent to CCL by: &quot;Sayed =A0Mes&quot; [Elsayed.elmes]^[<a href=3D"http:/=
/yahoo.com" target=3D"_blank">yahoo.com</a>]<br>
Dear Subscribers,<br>
I preformed scaling for &quot;Geometry optimization (only 4 steps)&quot; an=
d &quot;Single point Scaling&quot; for first row transition metal complex w=
ith 1,2,4 and 8 cores on MPI cluster. DFT method is used for this purpose. =
I found that there is no difference among them; i.e. the time consuming wit=
h 1 core is nearly the same like 2 or 4 or 8 cores.<br>

<br>
Anybody know why there is no difference in consuming time among them?<br>
<br>
=A0Thanks,<br>
Sayed<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br> =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0 <br> =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 7.05, School of Chemistry,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi=
ty of Manchester,<br>
 =A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL, <br> =A0 =A0 =A0 =A0 =A0=
 =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.<br><br> =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0Home Address<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
Chemistry Department,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o=
f Science,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers=
ity,<br>
 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,<br> =A0 =
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m.net</a><br>
 =A0 =A0 =A0 =A0 =A0 =A0 =A0Website: <a href=3D"http://www.compchem.net">ww=
w.compchem.net</a><br> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623=
42601<br>
</div>

--0016e6d784e34f83fd04801f4442--


From owner-chemistry@ccl.net Sun Feb 21 15:32:01 2010
From: "Mahmoud A. A. Ibrahim m.ibrahim*compchem.net" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL:G: True energy of transition state
Message-Id: <-41305-100221121953-22247-DxIN5vXroNNfWZXCVuYnXw^_^server.ccl.net>
X-Original-From: "Mahmoud A. A. Ibrahim" <m.ibrahim|a|compchem.net>
Content-Type: multipart/alternative; boundary=001485f1dcea778bcf04801f85ec
Date: Sun, 21 Feb 2010 17:19:38 +0000
MIME-Version: 1.0


Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim _ compchem.net]
--001485f1dcea778bcf04801f85ec
Content-Type: text/plain; charset=ISO-8859-1

Dear Matthew
You may take Chapter 4 in "Exploring chemistry with electronic structure
methods" as a *start *point, and what follow depends on your system and
model chemistry used/going to be used.
There is one point, you *couldn't *scale the thermodynamic outputs. You *have
to *include the scale factor in your job, where the frequencies are scaled
by your implemented factor before performing the thermodynamic analysis.
Sincerely;
M. Ibrahim

On Sun, Feb 21, 2010 at 2:12 PM, Matthew Tassell mtassell!=!gmail.com <
owner-chemistry_-_ccl.net> wrote:

>
> Sent to CCL by: "Matthew   Tassell" [mtassell(-)gmail.com]
> Dear CCL
>
> I have recently been trying to calculate the barrier heights for a reaction
> between a aldehyde radical and double bond.
>
> When i look at the thermochemistry data for the transition state i'm not
> entirly sure how to go about taking into consideration various corrections,
> zero-point etc.
>
> I have searched the CCl site, internet and read the gaussian
> thermochemistry white paper but still not sure how to go about finding the
> answer.
>
> If anybody has experience in these matters and could point me in the right
> direction i would be very grateful.
>
> Many thanks in advance>
>
>


-- 
                 Mahmoud A. A. Ibrahim
                      Current Address
                7.05, School of Chemistry,
             The University of Manchester,
        Oxford Road, Manchester, M13 9PL,
                      United Kingdom.

                       Home Address
                 Chemistry Department,
                    Faculty of Science,
                       Minia University,
                          Minia 61519,
                               Egypt.

                    Contact Information
          Email: m.ibrahim_-_compchem.net
             Website: www.compchem.net
                  Fax No.: +20862342601

--001485f1dcea778bcf04801f85ec
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Matthew<div>You may take Chapter 4 in &quot;Exploring chemistry with e=
lectronic structure methods&quot; as a <b>start </b>point, and what follow =
depends on your system and model chemistry used/going to be used.</div><div=
>
There is one point, you <b>couldn&#39;t </b>scale the=A0thermodynamic=A0out=
puts. You <b>have to </b>include the scale factor in your job, where the fr=
equencies are scaled by your implemented factor before performing the therm=
odynamic analysis.</div>
<div>Sincerely;</div><div>M. Ibrahim<br><br><div class=3D"gmail_quote">On S=
un, Feb 21, 2010 at 2:12 PM, Matthew Tassell mtassell!=3D!<a href=3D"http:/=
/gmail.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-che=
mistry_-_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;"><br>
Sent to CCL by: &quot;Matthew =A0 Tassell&quot; [mtassell(-)<a href=3D"http=
://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Dear CCL<br>
<br>
I have recently been trying to calculate the barrier heights for a reaction=
 between a aldehyde radical and double bond.<br>
<br>
When i look at the thermochemistry data for the transition state i&#39;m no=
t entirly sure how to go about taking into consideration various correction=
s, zero-point etc.<br>
<br>
I have searched the CCl site, internet and read the gaussian thermochemistr=
y white paper but still not sure how to go about finding the answer.<br>
<br>
If anybody has experience in these matters and could point me in the right =
direction i would be very grateful.<br>
<br>
Many thanks in advance<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br> =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0 <br> =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0=
 =A0 7.05, School of Chemistry,<br> =A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi=
ty of Manchester,<br>
 =A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL, <br> =A0 =A0 =A0 =A0 =A0=
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</div>

--001485f1dcea778bcf04801f85ec--


From owner-chemistry@ccl.net Sun Feb 21 16:07:00 2010
From: "Prasenjit SEAL prasenjit.seal+*+crm2.uhp-nancy.fr" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL:G: G03 Temperature Parameter
Message-Id: <-41306-100221075102-18324-T5kqwylpXFWd1vtNbbRIvg.:.server.ccl.net>
X-Original-From: Prasenjit SEAL <prasenjit.seal a crm2.uhp-nancy.fr>
Content-Transfer-Encoding: 7bit
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Date: Sun, 21 Feb 2010 13:50:46 +0100
MIME-Version: 1.0


Sent to CCL by: Prasenjit SEAL [prasenjit.seal]![crm2.uhp-nancy.fr]
yahoo.com wrote:
> Dear All,
> I would like to know how I can enter the environment temperature in my 
> computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or 
> any other software you recommend.
>
> Thank you in advance.
> Best regards,
> A.F
>
>
Dear Arshad,

In Gaussian, one can set the temperature by writting *Temperature=???* 
(in K which is the default unit here) in the route section. By default, 
the temperature is 298.15K.

Cheers,
Prasenjit


From owner-chemistry@ccl.net Sun Feb 21 16:42:01 2010
From: "Soren Eustis soreneustis!A!gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: G03 Temperature Parameter
Message-Id: <-41307-100221160034-4577-njH0pmGbMe1Dg9Fnm0v9ww,+,server.ccl.net>
X-Original-From: Soren Eustis <soreneustis::gmail.com>
Content-transfer-encoding: quoted-printable
Content-type: text/plain;
	charset="ISO-8859-1"
Date: Sun, 21 Feb 2010 22:00:17 +0100
Mime-version: 1.0


Sent to CCL by: Soren Eustis [soreneustis * gmail.com]
Alexander,

  Nothing in Arash's posting suggests that he lacks knowledge in quantum
chemistry, thermodynamics, or computational chemistry for that matter.  He
simply does not know the requirements for G03 temperature input.  While I
would like to think have a solid background in all aspects of physical
chemistry, I often struggle with the rigid requirements of program input
parameters. Making this list inaccessible to all but the most expert users
does little to serve the community as a whole.


--=20
Dr. Soren N. Eustis
ETH =AD Zurich
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren=env.ethz.ch



On 2/21/10 8:05 AM, "Alexander Bagatur yants bagaturyants|-|gmail.com"
<owner-chemistry=ccl.net> wrote:

>=20
> Sent to CCL by: "Alexander Bagatur'yants" [bagaturyants-*-gmail.com]
> Dear All,
> I believe that letters should be somehow filtered before posting in the l=
ist
> or some stricter rules should be established.
> Too much garbage has been appearing  in our list recently.
> As to this question, I would first recommend the addressee to learn quant=
um
> chemistry or at least physical chemistry before starting work with quantu=
m
> chemistry.
>=20
> Best regards,
>=20
> Prof. Alexander A. Bagatur'yants
> Photochemistry Center
> Russian Academy of Sciences
> ul. Novatorov 7a
> Moscow 119421 Russia
> Phone:  +7(495)9362588 (office)
>                  +7(916)5317022 (mobile)
> Fax:         +7(495)9361255
> e-mail: sasha%a%photonics.ru
>                bagaturyants%a%gmail.com
>=20
>> From: owner-chemistry+sasha=3D=3Dphotonics.ru%a%ccl.net
> [mailto:owner-chemistry+sasha=3D=3Dphotonics.ru%a%ccl.net] On Behalf Of Arash
> yahoo.com
> Sent: Sunday, February 21, 2010 9:21 AM
> To: Bagaturyants, Alexander A.
> Subject: CCL:G: G03 Temperature Parameter
>=20
> Dear All,
> I would like to know how I can enter the environment temperature in my
> computations (i.e. Optimization, Energy, HOMO, etc. ) in Gaussian or any
> other software you recommend.
>=20
> Thank you in advance.
> Best regards,
> A.F
>=20
>=20
>=20
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From owner-chemistry@ccl.net Sun Feb 21 17:17:01 2010
From: "Marcel Swart marcel.swart ~~ icrea.es" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: G03 Temperature Parameter
Message-Id: <-41308-100221170823-32466-lOoBmwHePe0LzTpODSHIFQ]~[server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart * icrea.es>
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Date: Sun, 21 Feb 2010 23:07:56 +0100
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Sent to CCL by: Marcel Swart [marcel.swart:_:icrea.es]

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In any quantum-chemistry program, the temperature one can set on input =20=

has effect mainly
on the thermodynamic analysis, i.e. how the vibrational frequencies =20
can be transformed into
enthalpy, entropy and free energy.

The electronic energy, HOMO, LUMO, optimization, etc. are completely =20
independent of the
temperature.

Please read a good introductory textbook like Jensen's "Introduction =20
to computational chemistry",
or any one of the introductory textbooks (Szabo/Ostlund, McWeeny, =20
Leach, Cramer, etc.).

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
dr. Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica Computacional
Universitat de Girona

Parc Cient=EDfic i Tecnol=F2gic
Edifici Jaume Casademont (despatx A-27)
Pic de Peguera 15
17003 Girona
Catalunya (Spain)

tel
+34-972-183240
fax
+34-972-183241
e-mail
marcel.swart ~~ icrea.es
marcel.swart ~~ udg.edu
web
http://www.marcelswart.eu
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<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; "><div><br></div>In any =
quantum-chemistry program, the temperature one can set on input has =
effect mainly<div>on the thermodynamic analysis, i.e. how the =
vibrational frequencies can be transformed into</div><div>enthalpy, =
entropy and free energy.</div><div><br></div><div>The electronic energy, =
HOMO, LUMO, optimization, etc. are <b>completely independent</b> of =
the</div><div>temperature.&nbsp;</div><div><br></div><div>Please read a =
good introductory textbook like Jensen's "Introduction to =
computational&nbsp;chemistry",</div><div>or any one of the introductory =
textbooks (Szabo/Ostlund, McWeeny, Leach, Cramer, =
etc.).</div><div><div><div><font class=3D"Apple-style-span" =
size=3D"3"><span class=3D"Apple-style-span" style=3D"font-size: =
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normal normal 12px/normal Helvetica; =
">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; ">dr. Marcel Swart</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
min-height: 14px; "><br></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; ">ICREA Research Professor =
at</div><div style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: =
0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">Institut de Qu=EDmica Computacional</div><div style=3D"margin-top: =
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margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; ">Edifici Jaume Casademont (despatx =
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