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On 1/04/2011 2:06 PM, Sai Pooja wrote:
<blockquote
cite="mid:AANLkTimuCHSQqEqP4U6pyvVLqcMRqqDmqr94ciOrEagn@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Thu, Mar 31, 2011 at 10:41 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
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: 1px solid rgb(204, 204,
204); 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: 1px solid rgb(204, 204,
204); 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>
</div>
</blockquote>
<br>
Describing the overall objective is usually a good idea. Sometimes
one's candidate for a solution is not best and someone else knows it
:-) Here, energy groups are the only reasonable solution.<br>
<br>
Mark<br>
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