[gmx-users] Pulling simulation

Naveen BK naveenbk4717 at gmail.com
Mon Apr 8 08:20:27 CEST 2019

Dear all,

This question is regarding Umbrella sampling. My group 1 is substrate and
group 2 protein. Trying to pull the substrate molecule from the active site
pocket. In all the cases(for group 2), I used either atom or residue for
the center of mass [COM]. Now I want to run a simulation by considering
that COM of protein which may be present in the vacuum or in the empty
space. In other words, I don't want to fix any atom or residue of the
protein but I want to fix an empty space. I was not able to find any
solutions regarding this if anyone could help me to figure it, would be

Thanks and Regards,
Naveen Krishna
+91 8123474717

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