CCL: Heating Locally in MD

[David van der Spoel <spoel{:}xray.bmc.uu.se>]

 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
>  <div id="RTEContent">Dear CCLers,<br><br>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.&nbsp;
>  <br><br>I am wondering which MD package could that. If possible, I
>  prefer to free software such as TINKER. <br><br>Thank you very
>  much!<br><br></div><p>
> 		<hr size=1>Yahoo! Photos – Showcase holiday pictures in
>  hardcover<br>
>  <a href="http://us.rd.yahoo.com/mail_us/taglines/photobooks/*http://pa.yahoo.com/*http://us.rd.yahoo.com/mail_us/taglines/photos/evt=38088/*http://pg.photos.yahoo.com/ph//page?.file=photobook_splash.html";>Photo
>  Books</a>. 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
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++