[gmx-users] about the umbrella sampling potential

[Hao Jiang]

Dear all,

I got confused about the usage of pull-geometry and pull-dim (pull-vector)
settings in the umbrella sampling simulations (not the pull / SMD
simulations).

In an umbrella sampling potential, U(r)=0.5*(r-r0)*(r-r0), are r and r0
referring to (A) the distance between the pulled group and the reference
group, or (B) the distance between the pulled group and the reference group
*projected* to a vector pre-defined by pull-dim or pull-vector?

Note these two distances are not equal unless the pulled group stay strictly
on the predefined vector, which I believe is not always the case.

If A is true, in principle group1 should be able to move freely within a
spherical shell centered at group0, right? What is the point to specify
pull-geometry and pull-dim in this case?

If B is true, group1 should in principle be able to move freely in  plane
perpendicular to the pre-defined vector. So if pull-dim= N N Y, the pulled
group should be able to move freely in the X-Y plane, right?

Any help would be greatly appreciated!

Hao Jiang