[gmx-users] Umbrella sampling and PMF calculations

[Alex]

Just a few quick questions for Justin.

I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

1. In your example, you have two pull groups. My understanding is that both
are pulled relative to each other. In my case, the only thing that's pulled
to create the series of configurations required for WHAM is a single ion,
which is pulled relative to the rest of the system (nothing but a hydrated
membrane with a particular type of hole inside of it). The ion starts above
the hole, enters the hole, then leaves it, the aim here is to find the free
energy associated with sitting in that hole.
I recall (maybe incorrectly) that pull code has some quirks, so will your
procedure work, or is there anything I should be aware of?

2. It is my understanding that only pullx and pullf files are required for
WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files? May
I just clean those up in my script, or will they be needed at any point?

Thank you,

Alex