[gmx-users] distance/direction PMF

[Gavin Melaugh]

Hi all

Could someone please get back to me on this. I have ran two sets of
umbrella sampling simulations
1- Using pull_geometry = distance, and pull_dim = Y Y Y
2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125
0.735968
 
In both cases I wish to calculate the PMF for taking a host out of a
guest. I specify the distance between the COM of the two groups in the
respective mdp files. The two curves I get are completely different
which has leads me to ask a couple of questions:

1) Does the vector change as the dynamics evolves (i.e is it just
relative between the two points) or does it remain fixed in space?

2) Using umbrella sampling in the second case does the relative position
of the pull group (guest) fluctuate about the distance along the
specified vector?

Note- I couldn't run g_wham with pull_geometry = direction in my current
version of gromacs, so I ran it in 4.5.3 but I had to use the -if
pullf-files.xvg option.

Some help would be appreciated as I have to be sure of what the program
is actually doing.

Many thanks

Gavin