[gmx-users] Distance for window spacing in US?

Yun Shi yunshi09 at gmail.com
Wed Feb 20 07:14:50 CET 2013

Hi all,

For the purpose of calculating deltaG from umbrella sampling, I have
first pulled my ligand away from the enzyme active site along an
arbitrary direction (say x axis), setting the enzyme as pull_group0.

But I found the ligand was moving in the yz plane while pulling along
x, which I guess is not uncommon. Then I wonder which distance to use
a reference for the definition of umbrella sampling windows. Would
that be better to stick to the x component of protein-ligand distance,
which I can easily read from pullx.xvg file while ignoring the y and z
components? Or is it still better to use g_dist to calculate the
absolute protein-ligand COM distance and use it for spacing reference?


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