<br><br><div class="gmail_quote">On Wed, May 16, 2012 at 4:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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"><br>
<br>
On 5/16/12 11:16 AM, Steven Neumann wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
<br>
<br>
On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
On 5/16/12 10:25 AM, Steven Neumann wrote:<br>
<br>
Dear Justin,<br>
<br>
I pulled my ligad away of 6nm from the protein and obtained beautiful<br>
and smooth<br>
curve of PMF using 28 windows. Starting from zero kcal/mol corresponding<br>
to app<br>
0.3 nm then minima and curve increase till my plateau which starts from<br>
app 1 nm<br>
- then I have nearly straight line till 6.3 nm.<br>
My question: Can I decrease pulling distance to save time for the future<br>
simualtions with this system in terms of number of water molecules?<br>
Shall I just<br>
pull it away of 2-3 nm and I will obtain the same deltaG?<br>
<br>
<br>
Ideally, one would separate the molecules such that they are no longer<br>
interacting. Obviously with methods like PME this is impossible, so what<br>
you're after is sufficient separation such that there is negligible<br>
interaction between the protein and ligand. The required distance depends<br>
on the nature and size of the ligand, the types of interactions it<br>
experiences, and the cutoffs used. Keep in mind that even if a molecule is<br>
beyond the longest nonbonded cutoff, there are still effects like water<br>
ordering that can persist up to about 1.0 nm, so I would certainly make sure<br>
that all the atoms of the ligand and protein are separated by a minimum of<br>
twice the longest cutoff or so to account for this effect. Note that this<br>
would imply the use of g_mindist, not g_dist, as the distance I'm talking<br>
about is not the same as the COM distance.<br>
<br>
That's just my own rule of thumb for an initial check; you'll have to<br>
analyze your own system to decide what's happening and what you should do.<br>
<br>
-Justin<br>
<br>
<br>
Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away and<br>
obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till 3.5 nm<br>
(not till 6.3 nm) and I will obtain the same value it means that I can decrease<br>
the pulling distance in future simulations. Am I right?<br>
<br>
</div></div></blockquote>
<br>
In theory, as long as you've satisfied yourself that this constitutes a sufficient representation of a non-interacting state, or as close to it as one can achieve in a system of finite size. I've already said what I think are reasonable criteria for a preliminary assessment; it's up to you to convince anyone reading your work that such measurements are sound and appropriate.<span class="HOEnZb"><font color="#888888"><br>
<br>
-Justin</font></span></blockquote><div><br>Thanks. Well, as my cutoff is 1.4 nm pulling 3.5 nm will suffice - and having the same value in the example makes reasonable argument for pulling e.g. 4nm to be on the safe side.<br>
<br>Steven<br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="HOEnZb"><div class="h5"><br>
<br>
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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