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

[neeru sharma]

Dear Christopher Neale,

Let me re-frame my question again.
Though I am new to US, but I have a basic idea about performing US. My
main query lies for these 2 H-bonds:  one between Protein and MG and
other one between protein and GTP.

I want to know if I can perform umbrella sampling to explain the
formation of these 2 H-bonds too, as I have to perform WHAM analysis
too.
My systems initial configuration: Prot-Mg-GTP complex (both the H bonds absent)
Final configuration: Prot-Mg-GTP complex (both the H bonds present).

I want to explain the formation of these bonds using US, but don't
really know how to do it?


Any suggestion is always welcome.

Thanks and Regards,

Neeru



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,
Neeru