<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><font color="#ff0000"><span style="color: rgb(0, 0, 0);">Hi </span><span style="color: rgb(0, 0, 0);">all:</span> <br><br><span style="color: rgb(0, 0, 0);">I have been trying to figure out a problem in our umbrella sampling simulation. We are simulating a coarse grained protein passing through a coarse grained lipid bilayer. In the pull simulation, the protein was made to move from +z=6 nm of the box through the lipid layer at z=0 to z= -4 nm. For umbrella sampling 74 windows where chosen with a 0.2 nm. When we look at the histogram from the g_wham, we get good overlap before the protein touches the bilayer and after it has exited the bilayer. We also get the PMF curves for these regions.</span><br style="color: rgb(0, 0, 0);"><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">However, when the the protein
is in contact, and barely touching the bilayer, the g_wham analysis gives 0.000E+0 for PMF and no histograms in the output. We have tried decreasing the window size from 0.2 to 0.1 nm but it does not help. </span><br style="color: rgb(0, 0, 0);"><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">I looked at the gmx-user list to find a possible solution to this issue but could not find any helpful clue. Could anyone point me to what should be done and what is possibly going wrong?</span><br style="color: rgb(0, 0, 0);"><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">Thanks,</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">SNC</span><br></font></div></body></html>