[gmx-users] g_wham issue

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Aug 25 17:28:37 CEST 2011

Please provide very much more information. Unless somebody has run  
into the exact thing that you are describing it is currently  
impossible for us to help you.

One thing I can suggest now is to construct histograms of the sampling  
from the coord.xvg files yourself with some scripting and plot them  
all together to see if you have some regions with no overlap (but even  
still, please address my first point).

-- original message --

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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