<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Jan 23, 2012, at 1:00 PM, Mark Abraham wrote:</div><blockquote type="cite"><div><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></div></blockquote></div><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 40px; border: none; padding: 0px;"><div><a name="pull" style="color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -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 name="pull" style="color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 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><div><div><a name="pull" style="color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); font-size: medium; "><dd><dl compact=""><dt><b>position</b></dt></dl></dd></a></div></div><div><div><a name="pull" style="color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); font-size: medium; "><dd><dl 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></div><div><div><a name="pull" style="color: rgb(0, 0, 0); font-family: Times; font-style: normal; font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); font-size: medium; "><dd><dl compact=""><dd style="font-weight: normal; ">…...</dd></dl></dd></a></div></div></blockquote><div><div><div><br></div></div></div></body></html>