I actually understood your tutorial perfectly well. What I didn't expect
is such a significant dependence on direction (assuming spherical
symmetry clears the situation).
I also had to use direction-periodic instead of distance in your
tutorial, because the box is 4 nm wide and grompp is screaming about
distance exceeding half-box size. I used 5.0.3 before and it was fine
with the 'distance' directive. I think 'direction-periodic' is also
wrong for spherical symmetry. So, stick with distance and increase box size?
Thanks,
Alex
On 3/12/2018 1:35 PM, Justin Lemkul wrote:
On 3/12/18 3:28 PM, Alex wrote:
Thanks!
Just to make sure I'm doing this right this time. By merely changing
the dim directive with everything else following your tutorial, I
would be probing the spherical domain around the pore with a bunch of
different radius values? Because this is exactly what I want.
Yes, you're applying a 1-D bias when you actually want a 3-D bias.
People often misuse the tutorial .mdp files, though I will have a new
version of the tutorial out this summer (along with a paper) that
should clear all this up.
-Justin
Thanks,
Alex
On 3/12/2018 8:43 AM, Justin Lemkul wrote:
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
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