From owner-chemistry@ccl.net Fri Apr 21 08:51:00 2006
From: "Alex Allardyce aa|a|chemaxon.hu" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Program announcement and call for participants: ChemAxon UGM
Message-Id: <-31572-060421084825-941-/ZxpWnhJm1+i0bjWcj837w^server.ccl.net>
X-Original-From: "Alex  Allardyce" <aa+/-chemaxon.hu>
Date: Fri, 21 Apr 2006 08:48:20 -0400


Sent to CCL by: "Alex  Allardyce" [aa|-|chemaxon.hu]
Please excuse multiple postings

We are announcing the program and a call for participants at ChemAxon's 2006 User Group Meeting taking place June 7-8th at the Danubius Gellert Hotel, Budapest, Hungary.

The meeting will have a wide range of scientific and technical oral and poster presentations from ChemAxon users, partners and ChemAxon staff. This year we introduce parallel Scientific and Developer workshop sessions for hands on works. The final program is available here: http://www.chemaxon.com/UGM/06/program.html 

Those interested in participation should submit their registration, links below. The Poster abstract deadline remains open until May 26th. The event hotel is requesting priority booking for attendees, block bookings are held until April 28th.

I look forward to welcoming you to Budapest in June.

Alex

Meeting home page: http://www.chemaxon.com/UGM/06/index.html
Event program: http://www.chemaxon.com/UGM/06/program.html
To register or submit a poster abstract: http://www.chemaxon.com/forum/ftopic272.html
Poster submission guidelines: http://www.chemaxon.com/forum/ftopic295.html
Accomodation booking: http://www.chemaxon.hu/forum/ftopic261.html

Alex Allardyce
ChemAxon
email aa * chemaxon.com
Tel. +361 453 2658


From owner-chemistry@ccl.net Fri Apr 21 12:47:00 2006
From: "Aaron Deskins nathaniel.deskins++pnl.gov" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: Localized atomic basis set versus plane-waves
Message-Id: <-31573-060421124536-16881-qg7wiMGDx65Y0TFj817OWw(0)server.ccl.net>
X-Original-From: "Aaron  Deskins" <nathaniel.deskins]^[pnl.gov>
Date: Fri, 21 Apr 2006 12:45:33 -0400


Sent to CCL by: "Aaron  Deskins" [nathaniel.deskins- -pnl.gov]
  A colleague and I were having a discussion the other day about the various approaches to periodic DFT calculations and their usefulness. One one hand you have programs like Crystal03 or Gaussian03 that used localized basis sets such as gaussians functions. The other approach is to use a plane-wave basis set which are non-localized and periodic in nature.
  What would you say the real limitations to either method are? Can both methods give the same results? Is efficiency the real difference between the two approaches?

  I look forward to your answers and ideas.

Thank you,

Aaron Deskins


From owner-chemistry@ccl.net Fri Apr 21 18:45:00 2006
From: "Michael K. Gilson gilson]=[umbi.umd.edu" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: how to prevent rotational motion in MD simulations
Message-Id: <-31574-060421184048-6352-duF2962qkoC5EMj4GI9nTw|*|server.ccl.net>
X-Original-From: "Michael K. Gilson" <gilson ~ umbi.umd.edu>
Content-transfer-encoding: 7BIT
Content-type: text/plain; format=flowed; charset=ISO-8859-1
Date: Fri, 21 Apr 2006 18:36:58 -0400
MIME-version: 1.0


Sent to CCL by: "Michael K. Gilson" [gilson a umbi.umd.edu]
If thermal energy is not shared among all the degrees of freedom, then 
your molecule is not properly equilibrating and removing rotation by an 
artificial method outside of the simulation will not solve the 
fundamental problem with the simulation.  I could easily imagine that 
there would be problems if you are running straight MD on a single 
molecule in vacuum; it is known this may not thermalize well. You might 
want to consider using Langevin dynamics, which adds random forces and 
viscous drag and should assure good thermalization.

Regards,
Mike

>  
>
>>Sent to CCL by: "Ana Celia Araujo Vila Verde" [avilaverde ..
>>engr.psu.edu]
>>This is a multi-part message in MIME format.
>>
>>------_=_NextPart_001_01C663C4.24D82D20
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>>Hi all,
>>=20
>>I'm doing molecular dynamics simulations of a single polymer chain in
>>a =
>>vacuum and the chain is spinning around its centre of mass. The code
>>I =
>>use already removes the translation of the centre of mass, but I am =
>>concerned that too much energy is passed onto the rotational degree
>>of =
>>freedom and not enough energy is kept at the vibrational DOFs of the
>>=
>>molecule, so I'd like to remove the rotational DOF also during the MD
>>=
>>simulation.
>>=20
>>Could anyone point me to either an article describing an algorithm or
>>to =
>>a freely available code that does this?=20
>>=20
>>Thank you,
>>=20
>>Ana Vila Verde
>>=20
>>(Penn State University, Department of Chemical Engineering)
>>
>>------_=_NextPart_001_01C663C4.24D82D20
>>Content-Type: text/html;
>>	charset="iso-8859-1"
>>Content-Transfer-Encoding: quoted-printable
>>
>><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"><HTML =
>>DIR=3Dltr><HEAD><META HTTP-EQUIV=3D"Content-Type"
>>CONTENT=3D"text/html; =
>>charset=3Diso-8859-1"></HEAD><BODY><DIV><FONT face=3D'Arial' =
>>color=3D#000000 size=3D2>Hi all,</FONT></DIV>=0A=
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>=0A=
>><DIV><FONT face=3DArial size=3D2>I'm doing molecular dynamics =
>>simulations of a =0A=
>>single polymer chain in a vacuum and the chain is spinning around its
>>=
>>centre of =0A=
>>mass. The code I use already removes the translation of the centre of
>>=
>>mass, but =0A=
>>I am concerned that too much energy is passed onto the rotational
>>degree =
>>of =0A=
>>freedom and not enough energy is kept at the vibrational DOFs&nbsp;of
>>=
>>the =0A=
>>molecule, so I'd like to remove the rotational DOF also during the MD
>>=0A=
>>simulation.</FONT></DIV>=0A=
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>=0A=
>><DIV><FONT face=3DArial size=3D2>Could anyone point me to either an =
>>article =0A=
>>describing an algorithm or to a freely available code that does this?
>>=0A=
>></FONT></DIV>=0A=
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>=0A=
>><DIV><FONT face=3DArial size=3D2>Thank you,</FONT></DIV>=0A=
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>=0A=
>><DIV><FONT face=3DArial size=3D2>Ana Vila Verde</FONT></DIV>=0A=
>><DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>=0A=
>><DIV><FONT face=3DArial size=3D2>(Penn State University, Department
>>of =
>>Chemical =0A=
>>Engineering)</FONT></DIV></BODY></HTML>
>>------_=_NextPart_001_01C663C4.24D82D20--
>>
>>
>>
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-- 
Michael K. Gilson, M.D., Ph.D.
CARB Fellow and Professor
Center for Advanced Research in Biotechnology
University of Maryland Biotechnology Institute
9600 Gudelsky Drive
Rockville, MD 20850
Voice: 240-314-6217
Fax:   240-314-6255
gilson<at>umbi.umd.edu