On 3/11/18 8:05 PM, Alex wrote:
Just to add to my question... The pull code for the umbrella sampling
from each of the N configs, as used in Justin's tutorial, is
pull_coord1_type = umbrella
pull_coord1_geometry = distance
pull_coord1_dim = N N Y
So, in each of the generated pullf and pullx files we sample a flat
slice at a given Z, and the reported forces and displacements are
along Z. What appears to be the reaction coordinate in our case is the
radius from the pore mouth, and one has to sample a set of hemispheres
from a series of radius values. Is this at all a possibility?
Yes, but not by following the tutorial. You'd need to use
pull_coord1_dim = Y Y Y to restrict the ions to a given radius around
the pore itself. As it is, you're probably underestimating entropic
contributions to the free energy.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.