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

Christopher Neale chris.neale at mail.utoronto.ca
Fri Jun 29 03:11:58 CEST 2012

Dear Neeru:

Please reformulate your question so that it is clear what you are asking. If your question is "how do I do US?" you are unlikely to get much help here beyond being directed to one of the US tutorials that you can find by a google search. If however, you know how to do US but have a particular question about some aspect of the formation of these H-bonds, then I'll note that I don't actually see any question on that topic in your post.

-- original message --

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!

Thanks and regards,

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