From owner-chemistry@ccl.net Tue Jan 17 04:03:01 2006 From: "David van der Spoel spoel(0)xray.bmc.uu.se" To: CCL Subject: CCL: Heating Locally in MD Message-Id: <-30528-060117034806-4722-RZfS+yqzoSRBmiJ9sYbjVQ[A]server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 17 Jan 2006 08:47:31 +0100 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel|,|xray.bmc.uu.se] Charles Hu umchhu~~yahoo.com wrote: > Sent to CCL by: Charles Hu [umchhu]=[yahoo.com] > --0-1539825457-1137445232=:78507 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear CCLers, > > I am novice user here and would like to do some molecular dynamics calculation of an enzyme, with special requirement that only heating a part of the protein and freeze the rest. i.e., after minimizing and equilibrating the whole protein at 10K, only thermalize the active site of the enzyme to 300K. > > I am wondering which MD package could that. If possible, I prefer to free software such as TINKER. > > Thank you very much! > GROMACS can do T coupling and/or freezing on multiple user defined sets of atoms http://www.gromacs.org > > > > --------------------------------- > Yahoo! Photos – Showcase holiday pictures in hardcover > Photo Books. You design it and we’ll bind it! > --0-1539825457-1137445232=:78507 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear CCLers,

I am novice user here and would like to do some molecular dynamics calculation of an enzyme, with special requirement that only heating a part of the protein and freeze the rest. i.e., after minimizing and equilibrating the whole protein at 10K, only thermalize the active site of the enzyme to 300K. 

I am wondering which MD package could that. If possible, I prefer to free software such as TINKER.

Thank you very much!

>

Yahoo! Photos – Showcase holiday pictures in hardcover
> Photo Books. You design it and we’ll bind it! > --0-1539825457-1137445232=:78507--> > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel[-]xray.bmc.uu.se spoel[-]gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++