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On 23/01/2012 11:14 PM, Trigo Mourino, Pablo wrote:
<blockquote
cite="mid:2011096E-B18D-4E97-AC27-B641A0C05E56@nmr.mpibpc.mpg.de"
type="cite"><br>
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<div>On Jan 23, 2012, at 1:00 PM, Mark Abraham wrote:</div>
<blockquote type="cite">
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<blockquote type="cite">Also I want to add to the Force term
a way to calculate an extra force<br>
</blockquote>
<blockquote type="cite">parameter which one atom is exerting
under their neighbors (as a derivative<br>
</blockquote>
<blockquote type="cite">regarding the new molecule-fixed
frame of reference absolute orientation).<br>
</blockquote>
<br>
I have no idea what you mean here.<br>
<br>
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</blockquote>
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<span class="Apple-tab-span" style="white-space:pre"> </span>The
idea is, the energy of a different orientations for one group of
atoms is generating a force under the neighbor atoms in the
molecule and we want to introduce that force in the simulation. As
far as I know is maybe something similar to the implementation of
pull code in umbrella sampling but with the difference that the
pull should be energy-driven and no restrained along a vector as
in:
<blockquote class="webkit-indent-blockquote" style="margin: 0 0 0
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<div><a moz-do-not-send="true" name="pull" style="color: rgb(0,
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-webkit-text-stroke-width: 0px; background-color: rgb(255,
255, 255); font-size: medium; font-weight: normal; "><dt><b>pull_geometry:</b></dt>
</a></div>
<div><a moz-do-not-send="true" name="pull" style="color: rgb(0,
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255, 255); font-size: medium; "><dt style="font-weight:
normal; "><b><span class="Apple-tab-span"
style="white-space:pre"> </span></b></dt>
</a>…..</div>
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<div><a moz-do-not-send="true" name="pull" style="color:
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<dl compact="compact">
<dt><b>position</b></dt>
</dl>
</dd>
</a></div>
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<div><a moz-do-not-send="true" name="pull" style="color:
rgb(0, 0, 0); font-family: Times; font-style: normal;
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255, 255); font-size: medium; "><dd>
<dl compact="compact">
<dd style="font-weight: normal; ">Pull to the position
of the reference group plus <b>pull_init</b> + time*<b>pull_rate</b>*<b>pull_vec</b>.</dd>
</dl>
</dd>
</a></div>
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<div><a moz-do-not-send="true" name="pull" style="color:
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<dl compact="compact">
<dd style="font-weight: normal; ">…...</dd>
</dl>
</dd>
</a></div>
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</blockquote>
</blockquote>
<br>
Something that actually is intra-molecular is probably best
implemented as an (atypical) "bonded" interaction - again, don't
touch the kernels. You need some way of working out what atoms will
interact with what other atoms.<br>
<br>
Mark<br>
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