From owner-chemistry@ccl.net Fri Oct 12 01:16:01 2012 From: "Vivek Sharma vivek.viv.sharma,gmail.com" To: CCL Subject: CCL: MD Simulations Message-Id: <-47754-121011085912-15130-zBwu9uFTZ/6Mv1OkQ6Z9qw!A!server.ccl.net> X-Original-From: Vivek Sharma Content-Type: multipart/alternative; boundary=e89a8f838d03dc0d1904cbc822e4 Date: Thu, 11 Oct 2012 15:59:05 +0300 MIME-Version: 1.0 Sent to CCL by: Vivek Sharma [vivek.viv.sharma.:.gmail.com] --e89a8f838d03dc0d1904cbc822e4 Content-Type: text/plain; charset=ISO-8859-1 Hello, I think this book is also very good - Understanding molecular simulations by Frenkel and Smit. Plus, in my opinion NAMD program is very easy to learn, set up, use and there is also a very good documentation for it. Please see : http://www.ks.uiuc.edu/Research/namd/ Membrane setup is also easily done in this program. best regards, ViV On 11 October 2012 01:13, Amy J Austin amy_jean_austin ~~ yahoo.com < owner-chemistry(_)ccl.net> wrote: > > 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! > > Amy> > > -- http://www.facebook.com/vivek.viv.sharma +358 50 5759 509 --e89a8f838d03dc0d1904cbc822e4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

I think this book is also very good - Understanding molecular= simulations by Frenkel and Smit.

Plus, in my opinion NAMD program i= s very easy to learn, set up, use and there is also a very good documentati= on for it. Please see : h= ttp://www.ks.uiuc.edu/Research/namd/
Membrane setup is also easily done in this program.

best regards,
ViV


On 11 October 2012 01:13, A= my J Austin amy_jean_austin ~~ yahoo.com <= span dir=3D"ltr"><owner-chemistry(_)ccl.net> wrote:

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 i= nitio 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 espe= cially interested in docking calculations to membranes, but with a ligand (= small molecule) that hasn't been previously parametrized.

Thanks in advance!

Amy



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