From owner-chemistry@ccl.net Thu Oct 11 00:03:01 2012 From: "Savita Pundlik savita.pundlik^_^tcs.com" To: CCL Subject: CCL: packages Message-Id: <-47750-121010231257-17821-3NFRUlseiyP5otACz449wQ{}server.ccl.net> X-Original-From: Savita Pundlik Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1" Date: Thu, 11 Oct 2012 08:42:43 +0530 MIME-Version: 1.0 Sent to CCL by: Savita Pundlik [savita.pundlik.-,-.tcs.com] Hello,

Depending on your system and hence the choice of pseud= opotentials you would like to exercise,
there is Quantum Espresso (ultr= a-soft) and Abinit (norm-conserving), both free!
There may be others equ= ally good, but the our experience with the above has been very good.
Thanks and good luck,

Savita Pundlik
= Tata Consultancy Services
Mailto: savita.pundlik-,-tcs.com
Website: http://www.tcs.com


-----owner-chemistry+savita.pundlik=3D=3Dtcs.com-,-ccl.net= wrote: -----
To: "Pu= ndlik, Savita Sunil " <savita.pundlik-,-tcs.com>
From: "quan= tum chem qchem66,gmail.com"
Sent by: owner-che= mistry+savita.pundlik=3D=3Dtcs.com-,-ccl.net
Date: 10/10/2012 05:15PM
S= ubject: CCL: packages

Sent to CCL by: "quantum  chem" [qchem66{=3D}gmail.com]
D= ear Members,
              I sha= ll be extremely thankful if someone could suggest me a free
software pa= ckage for calculating the following:

Density of states
Magnetic p= roperties
Band structures

Thanks in advance
qc



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From owner-chemistry@ccl.net Thu Oct 11 08:35:01 2012 From: "Gkourmpis, Thomas Thomas.Gkourmpis_-_borealisgroup.com" To: CCL Subject: CCL: MD Simulations Message-Id: <-47751-121011020730-27373-pSW5TVuO/oW7WPUf2+M8+Q-,-server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 11 Oct 2012 08:07:18 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis#borealisgroup.com] Amy Hi Molecular Dynamics is a huge area but in my opinion the best starting point will be the book by Allen & Tildisley called Computer Simulations of Liquids ( http://www.amazon.co.uk/Computer-Simulation-Liquids-M-Allen/dp/0198556454 ). It is very well written and covers a very broad area while giving a solid understanding of the underlying physics (the mathematics are also minimal if you are scared by those sort of things) There are also other books that are far more involved and specialised but I think Mike Allen's book is a very good starting point. In terms of software there are quite a few options available, some free of charge some under a licence. Check this entry in Wikipedia that gives a good overview of what is available http://en.wikipedia.org/wiki/Category:Molecular_dynamics_software Since I do not work with membranes and biomolecules I cannot really give you more detailed help on your particular area of interest, but I am sure other members with similar research interests will pop up and help you. I hope this was helpful but if you need anything more just give us a shout Thomas Thomas Gkourmpis Researcher - Innovation & Technology Borealis AB | SE-444 86 Stenungsund | Sweden Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 www.borealisgroup.com | 556078-6633 | Swedish Companies Registration Office ___________________________________ Borealis - Shaping the Future with Plastics -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com:+:ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com:+:ccl.net] On Behalf Of Amy J Austin amy_jean_austin ~~ yahoo.com Sent: Thursday, October 11, 2012 12:14 AM To: Gkourmpis, Thomas Subject: CCL: MD Simulations Sent to CCL by: "Amy J Austin" [amy_jean_austin_-_yahoo.com] Greetings CCLer's, I would be grateful to receive some information on the best possible way to branch out into molecular dynamics calculations - My background is in ab initio method development, especially with DFT. I'm wondering if people could share books, programs with instructional manuals, etc that they have found useful for background as well as more practical aspects. I'm especially interested in docking calculations to membranes, but with a ligand (small molecule) that hasn't been previously parametrized. Thanks in advance! Amyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Thu Oct 11 11:53:00 2012 From: "Billy McCann bwm0005^^^tigermail.auburn.edu" To: CCL Subject: CCL: MD Simulations Message-Id: <-47752-121011104207-9875-ndbYucavkZiIEopqY6LTlw]^[server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 11 Oct 2012 14:41:49 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005##tigermail.auburn.edu] Hi Amy. A good introduction is given in Leach's Molecular Modelling. The "Further Reading" section of the chapter dealing with MD has excellent references. http://amzn.com/0582382106 Also, the Amber package has been given a thorough review in WIREs. WIREs Comput Mol Sci 2012. doi: 10.1002/wcms.1121 You may also be interested in: Studies in Molecular Dynamics. I. General Method, B. J. Alder and T. E. Wainwright J. Chem. Phys. 31, 459 (1959) doi: 10.1063/1.1730376 Hope that helps. Billy ****************************** Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Research Auburn University, Alabama, USA Office # = 1-334-844-6948 bwayne on irc.freenode.net ****************************** -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu[a]ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu[a]ccl.net] On Behalf Of Amy J Austin amy_jean_austin ~~ yahoo.com Sent: Wednesday, October 10, 2012 5:14 PM To: Billy McCann Subject: CCL: MD Simulations Sent to CCL by: "Amy J Austin" [amy_jean_austin_-_yahoo.com] Greetings CCLer's, I would be grateful to receive some information on the best possible way to branch out into molecular dynamics calculations - My background is in ab initio method development, especially with DFT. I'm wondering if people could share books, programs with instructional manuals, etc that they have found useful for background as well as more practical aspects. I'm especially interested in docking calculations to membranes, but with a ligand (small molecule) that hasn't been previously parametrized. Thanks in advance! Amyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Oct 11 12:33:00 2012 From: "Wendy A Warr wendy---warr.com" To: CCL Subject: CCL: 8th German Conference on Chemoinformatics Message-Id: <-47753-121011123133-31537-mcAn6TjSpmTqBmqSIVIYng(0)server.ccl.net> X-Original-From: "Wendy A Warr" Date: Thu, 11 Oct 2012 12:31:32 -0400 Sent to CCL by: "Wendy A Warr" [wendy(a)warr.com] 8th German Conference on Chemoinformatics. November 11 13, 2012, Goslar Germany https://www.gdch.de/index.php?id=1400 The program is available at https://www.gdch.de/index.php?eID=tx_nawsecuredl&u=0&file=fileadmin/downloads/Veranstaltungen/Tagungen/CIC_2012/prog_gcc_2012.pdf&t=1350663789&hash=67c1997ab51838f01c3b6cc99bd3cba33add7168 Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./Fax +44 (0)1477 533837 wendy : warr.com http://www.warr.com