From owner-chemistry@ccl.net Thu Aug 12 00:44:01 2010
From: "sudipta sudipta.mml===gmail.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Calculation of enthalpy from NPT simulation
Message-Id: <-42510-100811145730-1133-jmWJBst3ye/jFmrLqtmOOQ_._server.ccl.net>
X-Original-From: sudipta <sudipta.mml=gmail.com>
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Date: Thu, 12 Aug 2010 00:27:23 +0530
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Sent to CCL by: sudipta [sudipta.mml{:}gmail.com]
--0016e68ce6f2e9631d048d90d139
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Hi All,
I have ran a NPT simulation for a liquid water system (TIP3P) model
by NAMD package and want to calculate enthalpy of the system at that
temperature. How shall I proceed? I have used lagevin dynamics for
temperature and pressure control. As I know the conserved quantity in NPT
ensemble is enthalpy. In the output file of the simulation it provides
kinetic energy and potential energy of the system. But the kinetic and
potential energy of extended part is not given their. How shall I extract
them from a output file.
If I calculate enthalpy as KE+PE+Pressure(ext)XdeltaV, then is it logical.
The Pressure(ext) is the external pressure and deltaV is the volume change
that given in .xst file.
Any suggestion will be highly appreciated.
Thanks and regards
Sudipta
--0016e68ce6f2e9631d048d90d139
Content-Type: text/html; charset=ISO-8859-1
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Hi All,<br>
=A0=A0=A0=A0=A0=A0 <br>
=A0=A0=A0=A0=A0=A0=A0 I have ran a NPT simulation for a liquid water system=
(TIP3P)
model by NAMD package and want to calculate enthalpy of the system at that =
temperature.
How shall I proceed? I have used lagevin dynamics for temperature and
pressure control. As I know the conserved quantity in NPT ensemble is
enthalpy. In the output file of the simulation it provides kinetic
energy and potential energy of the system. But the kinetic and
potential energy of extended part is not given their. How shall I
extract them from a output file. <br>
<br>
If I calculate enthalpy as KE+PE+Pressure(ext)XdeltaV, then is it
logical. The Pressure(ext) is the external pressure and deltaV is the
volume change that given in .xst file.<br>
<br>
Any suggestion will be highly appreciated.<br>
<br>
Thanks and regards<br>
Sudipta
--0016e68ce6f2e9631d048d90d139--
From owner-chemistry@ccl.net Thu Aug 12 08:28:00 2010
From: "neeraj m neerajmisra:+:hotmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: calculation
Message-Id: <-42511-100812082654-19913-75ebEpd6uPUe0w/xVHY//g-x-server.ccl.net>
X-Original-From: "neeraj m" <neerajmisra_._hotmail.com>
Date: Thu, 12 Aug 2010 08:26:52 -0400
Sent to CCL by: "neeraj m" [neerajmisra{:}hotmail.com]
HOW TO CALCULATE MAGNETIC MOMENT OF A NANOCLUSTER?
From owner-chemistry@ccl.net Thu Aug 12 09:54:01 2010
From: "Prasenjit SEAL prasenjit.seal_._crm2.uhp-nancy.fr" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL:G: Problem in determining the emission maxima using Gaussian 03
Message-Id: <-42512-100812082532-18085-wXyCtGP3xji3lkSM5J/xXA[-]server.ccl.net>
X-Original-From: Prasenjit SEAL <prasenjit.seal]_[crm2.uhp-nancy.fr>
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Date: Thu, 12 Aug 2010 14:25:23 +0200
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Sent to CCL by: Prasenjit SEAL [prasenjit.seal[a]crm2.uhp-nancy.fr]
This is a multi-part message in MIME format.
--------------060607090306070101010302
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Dear CCL users,
Can anyone help me how to find the emission maxima using _Gaussian 03_ ?
Thanks in advance,
Prasenjit
--
Prasenjit Seal
Post-Doctoral Research Fellow
CRM2
Universit� Henri Poincar� - Nancy I
B.P. 239
F-54506 Vandoeuvre-les-Nancy, France
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
</head>
<body bgcolor="#ffffff" text="#000000">
Dear CCL users,<br>
<br>
Can anyone help me how to find the emission maxima using <u>Gaussian 03</u>
?<br>
<br>
Thanks in advance,<br>
<br>
Prasenjit<br>
<pre class="moz-signature" cols="72">--
Prasenjit Seal
Post-Doctoral Research Fellow
CRM2
Université Henri Poincaré - Nancy I
B.P. 239
F-54506 Vandoeuvre-les-Nancy, France</pre>
</body>
</html>
--------------060607090306070101010302--
From owner-chemistry@ccl.net Thu Aug 12 10:47:01 2010
From: "John McKelvey jmmckel- -gmail.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: Basis set notation
Message-Id: <-42513-100812103233-31617-iuDx584H1PjfQPE3ZDf2wA**server.ccl.net>
X-Original-From: John McKelvey <jmmckel,,gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 12 Aug 2010 10:32:26 -0400
MIME-Version: 1.0
Sent to CCL by: John McKelvey [jmmckel|a|gmail.com]
I may be out of touch on this:
I take the basis set notation 6-31G(d,p) to be the same as 6-31G**.
The question is whether or not the notation 6-31G(d',p' ) is accepted
as an alternative for 6-31++G**, or is (d',p') a notation I'm just out
of touch on?
Thanks!
John
--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel_._gmail.com
From owner-chemistry@ccl.net Thu Aug 12 12:44:00 2010
From: "Kirk Peterson kipeters:+:wsu.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: Basis set notation
Message-Id: <-42514-100812123802-13744-53+o1hVeJM2XQqPXhbeUug[A]server.ccl.net>
X-Original-From: Kirk Peterson <kipeters . wsu.edu>
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Date: Thu, 12 Aug 2010 09:37:24 -0700
Mime-Version: 1.0 (Apple Message framework v1081)
Sent to CCL by: Kirk Peterson [kipeters{=}wsu.edu]
John,
I have never seen the notation (d',p') as an alias for ++G** and in my opinion it should
be discouraged. It's bad enough that (d,p) is used instead of ** (although I know this is
somewhat common practice).
regards,
Kirk
-------------------------
Kirk A. Peterson
Professor of Chemistry
Department of Chemistry
Washington State University
Pullman, WA 99164-4630
office: (509) 335-7867
fax : (509) 335-8867
email: kipeters]_[wsu.edu
web: http://tyr0.chem.wsu.edu/~kipeters/
On Aug 12, 2010, at 7:32 AM, John McKelvey jmmckel- -gmail.com wrote:
>
> Sent to CCL by: John McKelvey [jmmckel|a|gmail.com]
> I may be out of touch on this:
>
> I take the basis set notation 6-31G(d,p) to be the same as 6-31G**.
> The question is whether or not the notation 6-31G(d',p' ) is accepted
> as an alternative for 6-31++G**, or is (d',p') a notation I'm just out
> of touch on?
>
> Thanks!
>
> John
> --
> John McKelvey
> 10819 Middleford Pl
> Ft Wayne, IN 46818
> 260-489-2160
> jmmckel-#-gmail.com>
>
From owner-chemistry@ccl.net Thu Aug 12 13:40:01 2010
From: "Marcel Swart marcel.swart(a)icrea.es" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: Basis set notation
Message-Id: <-42515-100812133805-18449-ICFS+f7TlHn7g9ojR/Otow#server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart^^icrea.es>
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Date: Thu, 12 Aug 2010 19:37:57 +0200
Mime-Version: 1.0 (Apple Message framework v1081)
Sent to CCL by: Marcel Swart [marcel.swart()icrea.es]
I think the notation (d,p) is better suited than **
because it allows for extension to (2d,3p) or
whatever other combination. The alternative
in ** language would then be ***** ? Without
making it clear that double polarized basis
could also be used (2df, 3pd), etc.
Marcel.
On Aug 12, 2010, at 6:37 PM, Kirk Peterson kipeters:+:wsu.edu wrote:
> John,
>
> I have never seen the notation (d',p') as an alias for ++G** and in my opinion it should
> be discouraged. It's bad enough that (d,p) is used instead of ** (although I know this is
> somewhat common practice).
>
> regards,
>
> Kirk
>
> -------------------------
> Kirk A. Peterson
> Professor of Chemistry
> Department of Chemistry
> Washington State University
> Pullman, WA 99164-4630
===================================
dr. Marcel Swart
ICREA Research Professor at
Institut de Qu�mica Computacional
Universitat de Girona
Parc Cient�fic i Tecnol�gic
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
===================================
From owner-chemistry@ccl.net Thu Aug 12 14:15:01 2010
From: "Cuperlovic-Culf, Miroslava Miroslava.Cuperlovic-Culf]=[nrc-cnrc.gc.ca" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Software(s) for molecule modelling, QM/MM and QM
Message-Id: <-42516-100812123030-9666-MXttaBrSQBN0/JG4ts4VBg::server.ccl.net>
X-Original-From: "Cuperlovic-Culf, Miroslava" <Miroslava.Cuperlovic-Culf*|*nrc-cnrc.gc.ca>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
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Date: Thu, 12 Aug 2010 12:30:22 -0400
MIME-Version: 1.0
Sent to CCL by: "Cuperlovic-Culf, Miroslava" [Miroslava.Cuperlovic-Culf*nrc-cnrc.gc.ca]
Dear All,
We are considering setting up a computational chemistry facility. The primary interest would be in life sciences and would include steps for enhancing the drug discovery process including:
Macromolecule modeling (proteins, RNA/DNA, lipids);
small molecule (drug) modeling;
docking;
interaction simulations
I have my opinions on what would be the best but as I am a bit out of data on these tools I would very much appreciate the opinions of all of you.
We would like to optimize in terms of quality of calculations/user friendliness/price (in that order).
You opinions/suggestions/experiences would be greatly appreciated. I will compile the answers subsequently for the benefit of the whole group,
Sincerely,
Mira Cuperlovic-Culf
NRC, Canada
From owner-chemistry@ccl.net Thu Aug 12 14:50:01 2010
From: "John L Kulp jlk287*nyu.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: new experimental solvation data
Message-Id: <-42517-100812135246-833-59G+DNnuzv/WVZ3Bmt9D9A-#-server.ccl.net>
X-Original-From: "John L Kulp" <jlk287[A]nyu.edu>
Date: Thu, 12 Aug 2010 13:52:40 -0400
Sent to CCL by: "John L Kulp" [jlk287]^[nyu.edu]
Hello,
What are the best references for new experimental solvation data (small molecules and amino acids) within the last 5 years?
Thanks!
From owner-chemistry@ccl.net Thu Aug 12 15:25:01 2010
From: "Oellien, F (Frank) frank.oellien%x%sp.intervet.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Final Call For Papers - German Conference on Chemoinformatics
Message-Id: <-42518-100812120742-30652-aUjhZwSqjs+q/vte+kBStw+*+server.ccl.net>
X-Original-From: "Oellien, F (Frank)" <frank.oellien() sp.intervet.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
charset="iso-8859-1"
Date: Thu, 12 Aug 2010 18:07:27 +0200
MIME-Version: 1.0
Sent to CCL by: "Oellien, F (Frank)" [frank.oellien%a%sp.intervet.com]
Final CALL FOR PAPERS
6th German Conference on Chemoinformatics
Hotel 'Der Achtermann', Goslar, Germany
7 - 9 November 2010
Dear Colleagues,
This is the final Call for Papers for the 6. German Conference on Chemoinformatics (http://www.gdch.de/gcc2010) to be held in Goslar, Germany, November 7 - 9, 2010. You can still submit abstracts until August 13, 2010!!
Posters can still be submitted until August 31, 2010. Last minute posters can be submitted until October 9, 2010.
We are inviting the submission of abstracts for talks and posters in the following plenary sessions:
* Chemoinformatics and Drug Discovcery
* Chemical Information, Patents, and Databases
* Molecular Modelling
* Computational Material Science and Nanotechnology
In addition other highlights in the field of Computational Chemistry are also welcome.
Invited Speakers this year are:
* Colleen Fitzpatrick, Identifiers International, Huntington Beach, USA
* Gerhard Klebe, University of Marburg, DE
* Holger Gohlke, University of D�sseldorf, DE
* J�rgen Gmehling, University of Oldenburg, DE
* Hans Fraaije, University of Leiden, NL
* Wolfang Guba, Roche, Basel, CH
* Andrew R. Leach, GSK, Stevenage, UK
Visit the conference website at www.gdch.de/gcc2010 for more information or access directly the Call-for-Paper PDF http://www.gdch.de/vas/tagungen/tg/einlad5412.pdf
Frank Oellien
GDCh CIC Chair
Mit freundlichen Gr��en / With kind regards
Dr. Frank Oellien
BioChemInformatics Scientist
Intervet Innovation GmbH
Zur Propstei
55270 Schwabenheim, Germany
E-Mail: frank.oellien[A]sp.intervet.com
Phone: +49 (6130) 948 365
Fax: +49 (6130) 948 517
Home http://www.intervet.com
A subsidiary of Merck & Co., Inc., Whitehouse Station, NJ, USA
Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch�ftsf�hrer: Dr. Peter Schmid
From owner-chemistry@ccl.net Thu Aug 12 16:01:01 2010
From: "Jamin Krinsky jamink a berkeley.edu" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL:G: Basis set notation
Message-Id: <-42519-100812155928-20744-ZVPwqScAmXlHoZYl9Mq1eg::server.ccl.net>
X-Original-From: Jamin Krinsky <jamink%%berkeley.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Thu, 12 Aug 2010 12:59:12 -0700
MIME-Version: 1.0
Sent to CCL by: Jamin Krinsky [jamink*o*berkeley.edu]
Hi John,
Your answer is neither. The 6-31G(d',p' ) basis is just input format
for the 6-31G(double-dagger) basis, see G. A. Petersson and M. A.
Al-Laham, “A complete basis set model chemistry. II. Open-shell
systems and the total energies of the first-row atoms,” J. Chem.
Phys., 94 (1991) 6081-90.
Gaussian's website states:
6-31G†: Gaussian 09 also includes the 6-31G† and 6-31G‡ basis sets of
George Petersson and coworkers, defined as part of the Complete Basis
Set methods [Petersson88, Petersson91]. These are accessed via the
6-31G(d') and 6-31G(d',p') keywords, to which single or double diffuse
functions may also be added; f functions may also be added: e.g.,
6-31G(d'f), and so on.
So you could have 6-31++G(d',p'). Hope this helps.
Regards,
Jamin
On Thu, Aug 12, 2010 at 7:32 AM, John McKelvey jmmckel- -gmail.com
<owner-chemistry * ccl.net> wrote:
>
> Sent to CCL by: John McKelvey [jmmckel|a|gmail.com]
> I may be out of touch on this:
>
> I take the basis set notation 6-31G(d,p) to be the same as 6-31G**.
> The question is whether or not the notation 6-31G(d',p' ) is accepted
> as an alternative for 6-31++G**, or is (d',p') a notation I'm just out
> of touch on?
>
> Thanks!
>
> John
> --
> John McKelvey
> 10819 Middleford Pl
> Ft Wayne, IN 46818
> 260-489-2160
> jmmckel-#-gmail.com> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemistry/sub_unsub.shtml> http://www.ccl.net/spammers.txt>
>
>
--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink * berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu
From owner-chemistry@ccl.net Thu Aug 12 20:06:00 2010
From: "John McKelvey jmmckel%%gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL:G: Basis set notation
Message-Id: <-42520-100812181216-3930-EfSnuIES4i4+8Elo/U4gZg%%server.ccl.net>
X-Original-From: John McKelvey <jmmckel,+,gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=UTF-8
Date: Thu, 12 Aug 2010 18:12:07 -0400
MIME-Version: 1.0
Sent to CCL by: John McKelvey [jmmckel###gmail.com]
Jamin...
I agree... I was refereeing a paper and had not seen it before and
some one at CCL pointed it out in the Gaussian manual..
Thanks..
John
On Thu, Aug 12, 2010 at 3:59 PM, Jamin Krinsky jamink a berkeley.edu
<owner-chemistry(_)ccl.net> wrote:
>
> Sent to CCL by: Jamin Krinsky [jamink*o*berkeley.edu]
> Hi John,
>
> Your answer is neither. The 6-31G(d',p' ) basis is just input format
> for the 6-31G(double-dagger) basis, see G. A. Petersson and M. A.
> Al-Laham, “A complete basis set model chemistry. II. Open-shell
> systems and the total energies of the first-row atoms,” J. Chem.
> Phys., 94 (1991) 6081-90.
>
> Gaussian's website states:
> 6-31G†: Gaussian 09 also includes the 6-31G† and 6-31G‡ basis sets of
> George Petersson and coworkers, defined as part of the Complete Basis
> Set methods [Petersson88, Petersson91]. These are accessed via the
> 6-31G(d') and 6-31G(d',p') keywords, to which single or double diffuse
> functions may also be added; f functions may also be added: e.g.,
> 6-31G(d'f), and so on.
>
> So you could have 6-31++G(d',p'). Hope this helps.
>
> Regards,
> Jamin
>
> On Thu, Aug 12, 2010 at 7:32 AM, John McKelvey jmmckel- -gmail.com
> <owner-chemistry : ccl.net> wrote:
>>
>> Sent to CCL by: John McKelvey [jmmckel|a|gmail.com]
>> I may be out of touch on this:
>>
>> I take the basis set notation 6-31G(d,p) to be the same as 6-31G**.
>> The question is whether or not the notation 6-31G(d',p' ) is accepted
>> as an alternative for 6-31++G**, or is (d',p') a notation I'm just out
>> of touch on?
>>
>> Thanks!
>>
>> John
>> --
>> John McKelvey
>> 10819 Middleford Pl
>> Ft Wayne, IN 46818
>> 260-489-2160
>> jmmckel-#-gmail.com> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemistry/sub_unsub.shtml> http://www.ccl.net/spammers.txt>
>>
>>
>
>
>
> --
> Jamin L Krinsky, Ph.D.
> Molecular Graphics and Computation Facility
> 175 Tan Hall, University of California, Berkeley, CA 94720
> jamink : berkeley.edu, 510-643-0616
> http://glab.cchem.berkeley.edu> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemistry/sub_unsub.shtml> http://www.ccl.net/spammers.txt>
>
>
--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel(_)gmail.com
From owner-chemistry@ccl.net Thu Aug 12 20:41:02 2010
From: "Kadir Diri dirikadir!^!gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: "Shine a light" and "Laser" now in Russian
Message-Id: <-42521-100812173041-4017-u2nYegaYdw6e5JTUWQsuKA,+,server.ccl.net>
X-Original-From: Kadir Diri <dirikadir**gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 12 Aug 2010 14:27:36 -0700
MIME-Version: 1.0
Sent to CCL by: Kadir Diri [dirikadir[*]gmail.com]
Dear Colleagues,
Upon request we now have our short educational movies "Shine a light"
and "Laser" with Russian and Spanish subtitles:
http://iopenshell.usc.edu/howto/education/
If you would like to contribute in spreading the joy of science to the
non-expert masses all over the world by translating the script to other
languages, we can send you the script.
Enjoy!
kadir
---------------
Kadir Diri, PhD
Research Scientist
Department of Chemistry and iOpenShell Center
SSC #401
University of Southern California
Los Angeles, CA 90089-0482
--------------------------
Relativistic correction to Murphy's law:
Whether things can go wrong or not, depends on your frame of reference.