<br><br><div class="gmail_quote">On Wed, May 16, 2012 at 3:38 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="HOEnZb"><div class="h5"><br>
<br>
On 5/16/12 10:25 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin,<br>
<br>
I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth<br>
curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app<br>
0.3 nm then minima and curve increase till my plateau which starts from 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? Shall I just<br>
pull it away of 2-3 nm and I will obtain the same deltaG?<br>
<br>
</blockquote>
<br></div></div>
Ideally, one would separate the molecules such that they are no longer interacting. Obviously with methods like PME this is impossible, so what you're after is sufficient separation such that there is negligible interaction between the protein and ligand. The required distance depends on the nature and size of the ligand, the types of interactions it experiences, and the cutoffs used. Keep in mind that even if a molecule is beyond the longest nonbonded cutoff, there are still effects like water ordering that can persist up to about 1.0 nm, so I would certainly make sure that all the atoms of the ligand and protein are separated by a minimum of twice the longest cutoff or so to account for this effect. Note that this would imply the use of g_mindist, not g_dist, as the distance I'm talking 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 analyze your own system to decide what's happening and what you should do.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br></font></span></blockquote><div><br>Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away and obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till 3.5 nm (not till 6.3 nm) and I will obtain the same value it means that I can decrease the pulling distance in future simulations. Am I right? <br>
<br><br>Steven <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span class="HOEnZb"><font color="#888888">
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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>
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