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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
