<br>I took initial 300 as equilibration,Now it seems fine.<br>Thank you ..<br><br><div class="gmail_quote">On Tue, Jun 22, 2010 at 9:21 AM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Take that replica on the left that shows a bimodal histogram. Now plot a time series of the displacement: x-axis = time and y-axis = displacement along reaction coord. Is it jumping back and forth between two regions of sampling? Probably not... more likely it starts near one maximum and transitions to another maximum.<br>
<br>
If this is true then it simply means that you have not equilibrated enough. Run longer and cut some of the initial sampling.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
I am doing US . Yes, histograms of population densities along the reaction<br>
coordinate. Please find the pull settings. Sampled for 800ps.(nsteps =<br>
400000). Pull_init will vary for each frame, depends on the window spacing.<br>
<br>
pull = umbrella<br>
pull_geometry = position<br>
pull_dim = N N Y<br>
pull_start = no<br>
pull_nstxout = 10<br>
pull_nstfout = 10<br>
pull_ngroups = 1<br>
pull_group0 = U_ref<br>
pull_pbcatom0 = 0<br>
pull_group1 = r_C1<br>
pull_pbcatom1 = 0<br>
pull_init1 = 0 0 0.1<br>
pull_k1 = 1000<br>
pull_rate1 = 0<br>
pull_vec1 = 0 0 0<br>
<br>
Please check this link for my histograms<br>
<br>
<a href="https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en" target="_blank">https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en</a><br>
<br>
I would greatly appreciate our suggestions.<br>
<br>
Thank you,<br>
-Aswathy<br>
<br>
On Mon, Jun 21, 2010 at 8:14 PM, <chris.neale at <a href="http://utoronto.ca" target="_blank">utoronto.ca</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Please clarify:<br>
<br>
Are doing SMD or are you doing US? If you're doing SMD then you should not<br>
be using WHAM and you should not really be able to generate any sampling<br>
histograms.<br>
<br>
Are the histograms that you are referring to population densities of the<br>
sampling along your reaction coordinate?<br>
<br>
My guess -- if you're doing US -- is that you have some incorrect pull<br>
group settings. Bimodal distributions are indeed possible, but should<br>
require very long sampling times to achieve, and I doubt that you are at<br>
those times yet. Your Fc is fine. Post your pull settings.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
When i did the Umbrella sampling of frames from an SMD (of ligand<br>
transport), I am getting bimodal histograms in some cases.<br>
<br>
Do you think this is because , the force constant that i used is very low<br>
(i<br>
used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my<br>
PMF result? Do I need to repeat the sampling again with another pull_k1<br>
value(higher value)?<br>
</blockquote>
<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>