<div dir="ltr">Could I get some input on this?<br><br>I have a couple of cases for
rather polar molecules where decoupling and annihilation give me
statistical significant differences in hydration free energies. The
differences are not that large, but significant. I'm trying to find out
what's already been done to validate so I know how much time/effort to
spend testing to try and figure out if there is a problem here.<br>
<br>Thanks.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 30, 2013 at 1:25 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On 2013-04-30 18:02, David Mobley wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
In GROMACS 4.6 and later, there's now a new feature available to allow<br>
decoupling of solute molecules in free energy calculations. I wanted to<br>
inquire as to how Coulomb decoupling works, as I'm not clear.<br>
<br>
Specifically, imagine I'm running a calculation of the hydration free<br>
energy of a small molecule in water, and I decouple it (LJ and Coulomb)<br>
from its surroundings. What is the final reference state for the small<br>
molecule? Is it the small molecule interacting with periodic copies of<br>
itself in the gas phase (bad)? Or is it not interacting with periodic<br>
copies of itself either? If the latter, how is this achieved?<br>
</blockquote></div>
Good question, also one would like to be able to decouple a molecule only in the central box and not in the surrounding boxes. This does not make a difference for liquids but it does for crystals.<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
Since I'm not familiar with the Coulomb decoupling aspect and it is<br>
conceptually more complicated than LJ decoupling, I want to make sure I<br>
understand how it's supposed to be working.<br>
<br>
Thanks!<br>
David<br>
<br>
<br>
--<br>
David Mobley<br>
</div><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a> <mailto:<a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a>><br>
<a href="tel:949-385-2436" value="+19493852436" target="_blank">949-385-2436</a><br>
<br>
<br><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br>David Mobley<br><a href="mailto:dmobley@gmail.com" target="_blank">dmobley@gmail.com</a><br>949-385-2436<br>
</div>