[gmx-users] AFM pulling for PMF calculation

Nickle Fan nicklefan at gmail.com
Fri Aug 18 23:01:04 CEST 2006

Dear gmx-users:

I am attempting to calculate the PMF of a small molecule across a membrane.
I am using the AFM method (pulling in the z-direction). I find that during
the simulaiton, the small molecule moves not only in the pulling direction,
but also in the x- and y-direction.

Since Pulling_force = spring_constant * (pos_spring- pos_molecule), one
would need the full position (i.e., not just the z-coordinate) of the small
molecule. However, the pull code output  provides only the z-coordinate of
the molecule. Would this cause a problem, or I am missing something apparent
(e.g., I should really do a 3-D pulling)?


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060818/f76818e7/attachment.html>

More information about the gromacs.org_gmx-users mailing list