[gmx-users] g_wham issue

shikha nangia nshikha at yahoo.com
Thu Aug 25 16:51:34 CEST 2011

Hi all: 

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.

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. 

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?

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