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<div class="gmail_quote">On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">On 1/04/2011 1:30 PM, Sai Pooja wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi,<br>This is regarding the energygroups that one can use in the mdp file for tracking energy. Are these the groups defined in the index file?<br>
</blockquote><br></div>Yes, the groups are defined there (or created by default if an index file is not supplied) and specified as energy groups in the .mdp file.
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">I want to know if I can define a subset of atoms in the index file and track its energy.<br></blockquote><br>
</div>Yes. Whether it means anything is another matter.<br></blockquote>
<div> </div>
<div>Well the idea is to modify the hamiltonian for only a subset of atoms and apply hamiltonian replica exchange. I was hoping defining energy group could be a good way to apply this(obv it would requires other changes too).</div>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>Mark<br><font color="#888888">-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>