<div dir="ltr">Thanks Justin,<br><br>My goal is to keep certain part fixed and move only a few of the residues (case is like providing flexibility to the site of interest only).<br>SO , do I need to specify the residue using some index file ?<br>
or is there some other way to specify the part of molecule for position restraining ??<br><br><br>With Thanks,<br>Vivek<br><br><br><div class="gmail_quote">2008/10/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="Wj3C7c"><br>
<br>
vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi there,<br>
I want to run MD over a part of my molecule , for few residues only (not the whole molecule).<br>
Can I do it using GROMACS ?<br>
I searched for the online documentation and mailing list, but unable to get appropriate information.<br>
If somebody has already tried such things earlier, please suggest and direct me for appropriate link and address.<br>
<br>
</blockquote>
<br></div></div>
Well, if your goal is to keep certain parts fixed and allow others to move, probably the easiest way to do it is to apply position restraints to the "fixed" part.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
With Thanks,<br>
Vivek<br>
<br>
<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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