CCL: MD Simulations

 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
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 -----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
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