[gmx-users] Regarding umbrella sampling simulations along H-bonds

[neeru sharma]

Dear Gromacs Users,

I am simulating a system containing Protein-Mg-GTP complex.

I intend to perform the umbrella sampling on the system to calculate
PMF and to perform wham analysis.
I have generated a series of conformations for the umbrella sampling.
My main consideration is towards the 2 H-bonds: one between Protein
and MG and other one between protein and GTP. Both of these bonds were
absent during the start of the simulation but formed when the
simulation was completed.

Can anyone suggest me what parameters or pull_geometry shall I use, to
perform the same. Any suggestion is welcome!


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Thanks and regards,
Neeru