From owner-chemistry@ccl.net Tue Oct 21 07:37:01 2014
From: "Sebastian Kozuch seb.kozuch ~~ gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: Computer cluster
Message-Id: <-50620-141021073447-4446-tcLXl69FSuu0sw9l+6dd8A..server.ccl.net>
X-Original-From: Sebastian Kozuch <seb.kozuch^_^gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=utf-8; format=flowed
Date: Tue, 21 Oct 2014 14:34:35 +0300
MIME-Version: 1.0
Sent to CCL by: Sebastian Kozuch [seb.kozuch__gmail.com]
Dear colleagues,
As many of you have done several times, I need to buy a computer
cluster, and I was hoping to get some tips from experienced people.
The idea is to run mostly DFT jobs on rather big molecules, with some
heavy wave function calculations for benchmark analysis. I am probably
going for 2x12 core nodes, with 128GB RAM and SSD hard disks (~800 GB),
which I think is good for DFT jobs, but the memory and scratch will
probably be too small for couple cluster calculations. What would you
do, obviously considering that the budget is far from infinite? Any
advice will be appreciated.
Sincerely,
Sebastian
From owner-chemistry@ccl.net Tue Oct 21 11:38:00 2014
From: "Simon Cross simon.{=}.moldiscovery.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: SSC14 - Scandinavian Symposium on Chemometrics
Message-Id: <-50621-141021093316-7794-aNFWrOSxLbTqfvTpwaXihg{=}server.ccl.net>
X-Original-From: Simon Cross <simon=moldiscovery.com>
Content-Type: multipart/alternative;
boundary="------------070907040306070300080302"
Date: Tue, 21 Oct 2014 15:33:06 +0200
MIME-Version: 1.0
Sent to CCL by: Simon Cross [simon/./moldiscovery.com]
This is a multi-part message in MIME format.
--------------070907040306070300080302
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
Dear colleagues,
The SSC14 Organizing Committee cordially invites you to attend the 14th
Scandinavian Symposium on Chemometrics that will be held in Sardinia
(Italy) on *June **14th-17th, 2015*.
The SSC series are major scientific events that have been organized in
different cities in Northern Europe since 1988 (Lappeenranta, Finland).
They have a fascinating scope covering rational approaches in
chemometrics, cheminformatics, design, omics and related sciences and
worldwide attendance from both academia and industry.
In the SSC14 various practical applications of chemometric methods in
chemistry, biochemistry and chemical technology fields will be
presented, using classical and newly developed algorithms. Therefore the
symposium will touch upon the development and applications of
chemometrics methods in Pharmaceutical, Cheminformatics, Omics, Process
control, Analysis of chemical processes, Optimization and Food technology.
Besides the scientific aspects of the program you will have the
opportunity to visit some of the most charming places of the
Mediterranean in a wonderful resort close to the sea. It is our
intention to make this Symposium a memorable event for the attendees,
both scientifically and socially.
Please visit _http://www.ssc14.org/_ for further information about the
venue, the main topics and the important deadlines. We look forward to
welcoming you in Sardinia!
With best regards, the organizing committee
_
_
_http://www.ssc14.org <http://www.ssc14.org/>_
--------------070907040306070300080302
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<meta http-equiv="CONTENT-TYPE" content="text/html;
charset=ISO-8859-1">
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0.05cm;
background: #ffffff; line-height: 0.6cm" align="JUSTIFY">
<font color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB">Dear colleagues,<br>
<br>
</span></font></font></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0.05cm;
background: #ffffff; line-height: 0.6cm" align="JUSTIFY"><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB">The
SSC14 Organizing Committee cordially invites you to attend
the 14th
Scandinavian Symposium on Chemometrics that will be held
in Sardinia
(Italy) on </span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB"><b>June </b></span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US"><b>14th-17th, 2015</b></span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US">.
</span></font></font></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0.05cm;
background: #ffffff; line-height: 0.6cm" align="JUSTIFY">
<font color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB">The
SSC series are major scientific events that have been
organized in
different cities in Northern Europe since 1988
(Lappeenranta,
Finland). They have a fascinating scope covering rational
approaches
in chemometrics, cheminformatics, design, omics and
related
sciences and worldwide attendance from both </span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US">academia </span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB">and
</span></font></font></font><font color="#444444"><font
face="Arial Unicode MS, serif"><font size="3"><span
lang="en-US">industry.</span></font></font></font></p>
<p class="western" style="margin-bottom: 0.35cm" align="JUSTIFY"><font
face="Arial Unicode MS, serif"><font size="3"><span lang="en-US">In
the
SSC14 various practical applications of chemometric methods
in
chemistry, biochemistry and chemical technology fields will
be
presented, using classical and newly developed algorithms.
Therefore
the symposium will touch upon the development and
applications of
chemometrics methods in Pharmaceutical, Cheminformatics,
Omics,
Process control, Analysis of chemical processes,
Optimization and
Food technology.</span></font></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0.05cm;
background: #ffffff; line-height: 0.6cm" align="JUSTIFY">
<font color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB">Besides
the scientific aspects of the program you will have the
opportunity
to visit some of the most charming places of the
Mediterranean in a
wonderful resort close to the sea. It is our intention to
make this
Symposium a memorable event for the attendees, both
scientifically and socially.<br>
<br>
</span></font></font></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0.05cm;
background: #ffffff; line-height: 0.6cm" align="JUSTIFY">
<font color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US">Please
visit </span></font></font></font><font color="#0000ff"><span
lang="en-US"><u><a href="http://www.ssc14.org/"><font
color="#0068cf"><font face="Arial Unicode MS, serif"><font
size="3">http://www.ssc14.org/</font></font></font></a></u></span></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US"> for
further information about the venue, the main topics and
the
important deadlines. </span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-GB">We
look forward to welcoming you in Sardinia!</span></font></font></font></p>
<p class="western" style="margin-bottom: 0.18cm; background:
#ffffff; line-height: 0.18cm">
<font color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US"><span style="background:
#ffffff"><br>
With
best regards, the organizing committee</span></span></font></font></font><font
color="#444444"><font face="Arial Unicode MS, serif"><font
size="3"><span lang="en-US"></span></font></font></font></p>
<p class="western" style="margin-bottom: 0.18cm; background:
#ffffff; line-height: 0.18cm"><font color="#0000ff"><span
lang="en-US"><u><br>
</u></span></font></p>
<p class="western" style="margin-bottom: 0.18cm; background:
#ffffff; line-height: 0.18cm"><font color="#0000ff"><span
lang="en-US"><u><a href="http://www.ssc14.org/"><font
color="#0068cf"><font face="Arial Unicode MS, serif"><font
size="3"><span style="background: #ffffff">http://www.ssc14.org</span></font></font></font></a></u></span></font></p>
<title></title>
<meta name="GENERATOR" content="LibreOffice 3.5 (Linux)">
<style type="text/css">
<!--
^^page { margin: 2cm }
P { margin-bottom: 0.21cm; direction: ltr; color: #000000; widows: 2; orphans: 2 }
P.western { font-family: "Calibri", serif }
P.cjk { font-family: "Droid Sans"; so-language: en-US }
P.ctl { font-family: "Calibri" }
A:link { color: #0000ff; so-language: en-US }
-->
</style>
</body>
</html>
--------------070907040306070300080302--
From owner-chemistry@ccl.net Tue Oct 21 15:22:01 2014
From: "Zork Zou zorkzou.]*[.gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL:G: Isotope effects: is your thermochemistry calculation correct?
Message-Id: <-50622-141021151743-18601-zQuMaoQ4r5zjGyl+xG/jRA]*[server.ccl.net>
X-Original-From: Zork Zou <zorkzou^^gmail.com>
Content-Type: multipart/alternative; boundary=089e015369243023cf0505f3afea
Date: Tue, 21 Oct 2014 14:17:37 -0500
MIME-Version: 1.0
Sent to CCL by: Zork Zou [zorkzou^^^gmail.com]
--089e015369243023cf0505f3afea
Content-Type: text/plain; charset=UTF-8
In a quantum chemistry calculation, there may be two related symmetries:
the symmetry of nuclear charges (Sz) and the symmetry of atomic nuclei
(Sn). The former doesn't depend on atomic masses whereas the latter does.
Usually the two symmetries are the same, but in the case of isotope
substitution they can be different. For example, in H2O, both of them are
C2v, but in HDO they are C2v and Cs, respectively.
Symmetry may affect thermochemistry results significantly through the
rotational entropy (S_rot):
S_rot = 177.671 eu/mole + R * ln(T) + R * ln(I/s) ... (linear molecule)
or
S_rot = 267.643 eu/mole + (3/2) * R * ln(T) + R * ln[sqrt(I1 * I2 * I3)/s]
... (nonlinear molecule)
where "I" is the moment of inertia, and "s" is the symmetry number, which
"is defined as the number of indistinguishable positions into which the
molecule can be turned by simple rigid rotations". (see M. A. Paul,
Principles of chemical thermodynamics, 1951, p. 663)
Obviously, not only "I", but also "s" depends on the isotopes. However, by
checking the thermochemistry results of most quantum chemistry programs
including Gaussian, I found a wrong symmetry (Sz) being used for "s" by all
of them, so "s" is independent of isotopes by mistake. In the case of
isotopic substitution in high-symmetric molecule, this may lead to big
errors in the Gibbs free energy. For example, s=60 for fullerene C60 (Sz =
Sn = Ih) and s=1 if one carbon atom is replaced by C14 (Sz = Ih and Sn =
C1). At the PM6 level of theory and at 1 atm and 298.15 K, the thermal
corrections to Gibbs free energy are 0.351192 Hartree (s=60) and 0.347326
Hartree (s=1), that is, the error by using Ih symmetry is about 2.4
kcal/mol !!!
In the example above HDO, the error in Gibbs free energy is about 0.4
kcal/mol.
So, be careful with your thermochemistry calculations with isotopic
substitution.
--089e015369243023cf0505f3afea
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr"><div>In a quantum chemistry calculation, there may be two =
related symmetries: the symmetry of nuclear charges (Sz) and the symmetry o=
f atomic nuclei (Sn). The former doesn't depend on atomic masses wherea=
s the latter does. Usually the two symmetries are the same, but in the case=
of isotope substitution they can be different. For example, in H2O, both o=
f them are C2v, but in HDO they are C2v and Cs, respectively.</div><div><br=
></div><div>Symmetry may affect thermochemistry results significantly throu=
gh the rotational entropy (S_rot):</div><div><br></div><div>S_rot =3D 177.6=
71 eu/mole + R * ln(T) + R * ln(I/s) ... (linear molecule)</div><div><br></=
div><div>or</div><div><br></div><div>S_rot =3D 267.643 eu/mole + (3/2) * R =
* ln(T) + R * ln[sqrt(I1 * I2 * I3)/s] ... (nonlinear molecule)</div><div><=
br></div><div>where "I" is the moment of inertia, and "s&quo=
t; is the symmetry number, which "is defined as the number of indistin=
guishable positions into which the molecule can be turned by simple rigid r=
otations". (see M. A. Paul, Principles of chemical thermodynamics, 195=
1, p. 663)</div><div><br></div><div>Obviously, not only "I", but =
also "s" depends on the isotopes. However, by checking the thermo=
chemistry results of most quantum chemistry programs including Gaussian, I =
found a wrong symmetry (Sz) being used for "s" by all of them, so=
"s" is independent of isotopes by mistake. In the case of isotop=
ic substitution in high-symmetric molecule, this may lead to big errors in =
the=C2=A0Gibbs=C2=A0free energy. For example, s=3D60 for fullerene C60 (Sz =
=3D Sn =3D Ih) and s=3D1 if one carbon atom is replaced by C14 (Sz =3D Ih a=
nd Sn =3D C1). At the PM6 level of theory and at 1 atm and 298.15 K, the th=
ermal corrections to Gibbs free energy are 0.351192 Hartree (s=3D60) and 0.=
347326 Hartree (s=3D1), that is, the error by using Ih symmetry is about 2.=
4 kcal/mol !!!</div><div><br></div><div>In the example above HDO, the error=
in Gibbs free energy is about 0.4 kcal/mol.</div><div><br></div><div>So, b=
e careful with your thermochemistry calculations with isotopic substitution=
.<br></div></div>
--089e015369243023cf0505f3afea--