[gmx-users] PMF and g_wham

Stefan Hoorman stefhoor at gmail.com
Wed Oct 21 21:57:06 CEST 2009

While using g_wham to obtain a PMF from umbrella sampling simulations I came
up with the following problem. I have simulated my windows with a 0.1nm
difference between structures starting from the initial position where my
dimer is equilibrated and ending 0.5nm farther than what the lennard jones
and coulomb interactions between these structures exist. When I include all
these windows including the last 5 ones where my structures do not interact,
my profile.xvg comes out as a straight line at zero energy. The histogram
file looks fine, but the profile comes out wrong. When I do not include
these last 5 windows my profile comes out as expected but there seems to be
no final plateau. Is this normal in g_wham? Any advice on the matter would
be great.
Thank you
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