I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 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">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, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<div class="gmail_quote"><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 be using WHAM and you should not really be able to generate any sampling histograms.<br>
<br>
Are the histograms that you are referring to population densities of the sampling along your reaction coordinate?<br>
<br>
My guess -- if you're doing US -- is that you have some incorrect pull group settings. Bimodal distributions are indeed possible, but should require very long sampling times to achieve, and I doubt that you are at 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 (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><font color="#888888">
<br>
<br>
<br>
-- <br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>