From owner-chemistry@ccl.net Mon Jan 12 08:34:01 2015
From: "Stefan Grimme grimme[*]thch.uni-bonn.de" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: Molecular dynamics for metal complexes
Message-Id: <-50890-150112055353-26596-+/EbPwLwHMxpl7ZvwtHawg**server.ccl.net>
X-Original-From: "Stefan   Grimme" <grimme- -thch.uni-bonn.de>
Date: Mon, 12 Jan 2015 05:53:52 -0500


Sent to CCL by: "Stefan   Grimme" [grimme(0)thch.uni-bonn.de]
>Dear Stefan,
>An interesting approach- but if you already have a QM optimized structure and the corresponding Hessian what is the real benefit in seemingly 'reverting' to a FF, except for perhaps solving for a derivative model.  Some clarification (my re-education) will surely be appreciated.
>Thanks!
>Joseph 


Dear Joseph,
with "normal" computer resources and a standard DFT setup 
for a metal complex you are typically limited to a few hundred QM energy and 
force evaluations. With the corresponding FF, however, you 
can do millions of steps for e.g. MD. Also (automatic) conformational 
searches are rarely possible at a QM level while its quite routine
with QMDFF. Another advantage of the FF is that you can easily let 
many molecules interact e.g. in a liquid or solid (melting or explicit solvation). A further special feature of QMDFF is that it can break covalent bonds (simultaneously) which is non-trivial with usual (single-determinant) QM methods.
Hope this helps
Cheers!
Stefan


From owner-chemistry@ccl.net Mon Jan 12 09:09:01 2015
From: "Banck, Michael - michael.banck]^[ch.tum.de" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: Any regrets open-sourcing your programs?
Message-Id: <-50891-150112071426-2862-kB/Vla46ekgu9IX5VVTwTQ#%#server.ccl.net>
X-Original-From: "Banck, Michael -" <michael.banck++ch.tum.de>
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Date: Mon, 12 Jan 2015 13:14:18 +0100
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Sent to CCL by: "Banck, Michael -" [michael.banck],[ch.tum.de]
Hi,

On Sun, Jan 11, 2015 at 11:17:08AM +0100, uekstrom.:.gmail.com uekstrom.:.gmail.com wrote:
> Our situation is this: We have programs that are already distributed in
> source form free of charge, but with a special license agreement. We do not
> expect any serious contributions from people outside the current community
> just because we open source the program. (However, if the program is
> accepted into a major Linux distribution you get automatically free high
> quality testing and bug reports on many platforms).

Depending on which kind of program it is and how mature/generally useful
it is, I could help you get it into Debian/Ubuntu, my group is packaging
all the open source quantum chemistry codes for those distributions.

As a sidenote, my experience shows that just throwing something "over the
fence" by open sourcing it won't magically attract contributions.  There
are various degrees of openness:

1. Code being dropped on release, everything else is opaque to the
outside (ACESIII is an example of this, to the degree where users have
to figure out what changed on their own)

2. At least a user list available for questions/support (NWChem might
fit here, though regular development snapshots are provided and a
read-only subversion repository is public I believe)

3. Code repository available, but new features are developped in private
trees (this is quite common)

4. Developer list available, but some core discussions are possibly
off-list (in my experience public developer lists are mostly the case
for cheminformatics codes)

5. Everything in the open

I think as a research group, open sourcing your package will probably
not lead to immediate outside contributions by individuals in the core
areas (though people might send patches for the build system and
portability issues), but you get a shot at maybe other groups
contributing major features instead of writing their own code in the
future.

And yeah, maybe in the future it will be considered hazardous for group
leaders to keep development closed cause it will deny their staff to get
their contributions evaluated by external people when they apply for
jobs etc.


Michael


From owner-chemistry@ccl.net Mon Jan 12 12:38:01 2015
From: "Kaushik Hatua kaushikhatua[-]yahoo.in" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Ghost Atom
Message-Id: <-50892-150112123546-16844-aBQdCsXLxfYbbUO7dtoXLQ[a]server.ccl.net>
X-Original-From: Kaushik Hatua <kaushikhatua:_:yahoo.in>
Content-Type: multipart/alternative;
	boundary="_BB9CCEA3-5720-4E16-A923-D799CA164646_"
Date: Mon, 12 Jan 2015 23:05:35 +0530
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Sent to CCL by: Kaushik Hatua [kaushikhatua_._yahoo.in]
--_BB9CCEA3-5720-4E16-A923-D799CA164646_
Content-Transfer-Encoding: quoted-printable
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Dear all

Would anybody help me how to set ghost atom in g09. After the manual I foun=
d Bq but it has no basis function. For example in ethylene I want set one C=
H2 group as ghost atom having  same basis function like other CH2 group spe=
cified in route section.

Sent from Nokia Lumia =

--_BB9CCEA3-5720-4E16-A923-D799CA164646_
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html; charset="Windows-1252"

<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html; charset=
=3Dwindows-1252"></head><body><div><div style=3D"font-family: Calibri,sans-=
serif; font-size: 11pt;">Dear all<br><br>Would anybody help me how to set g=
host atom in g09. After the manual I found Bq but it has no basis function.=
 For example in ethylene I want set one CH2 group as ghost atom having&nbsp=
; same basis function like other CH2 group specified in route section.<br><=
br>Sent from Nokia Lumia </div></div></body></html>=

--_BB9CCEA3-5720-4E16-A923-D799CA164646_--


From owner-chemistry@ccl.net Mon Jan 12 14:56:01 2015
From: "David Sherrill prof.david.sherrill(-)gmail.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: Georgia Tech Summer Theory Program
Message-Id: <-50893-150112143037-29273-cpzOklGBIlSoH3KaWmOgiw^-^server.ccl.net>
X-Original-From: David Sherrill <prof.david.sherrill**gmail.com>
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Date: Mon, 12 Jan 2015 14:30:31 -0500
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Sent to CCL by: David Sherrill [prof.david.sherrill+/-gmail.com]
Georgia Tech will host its annual Summer Theory Program as part of its
NSF-sponsored Research Experiences for Undergraduates (REU) program in
chemistry and biochemistry.  The ten-week program runs from May 24 to
July 31 and is open to students who will be in their junior or senior
years during the next academic year.  Theory students will work with
Professors David Sherrill, Rigoberto Hernandez, or Angelo Bongiorno
in the areas of electronic structure theory, nonequilibrium dynamics, or
condensed-matter simulations.

The research experience is supplemented by an introductory lecture
series in theoretical chemistry.  Successful applicants will receive
a stipend of $5000, a travel allowance, and housing.  Further details
are available at

   http://vergil.chemistry.gatech.edu/opp/summer.html
and
   http://ww2.chemistry.gatech.edu/reu/

Participants supported by the NSF must be US citizens or permanent residents
of the US.

The deadline for applications is February 14.  Early applications are
encouraged.


C. David Sherrill, Ph.D.
Professor of Chemistry
Professor of Computational Science and Engineering