On 3/13/18 4:19 PM, Alex wrote:
What I meant is each of those files now has two columns, the first of which is of course time. What the second column is, especially for pullf, is a mystery to me. The total radial force? I wish someone who wrote the new pull

It's the force on the spring connecting the two groups.


code would clarify, because the result of wham now looks rather strange -- a long (1.5 nm!) hydration barrier for the ion. Makes little physical sense and very different from the bias along Z case.

I am guessing that the sampling of 1 ns per hemispherical slice is far from sufficient to probe that space... Just looked at one of the trajectories there -- the ion is nowhere near moving around the entire slice.


On 3/13/2018 10:27 AM, Justin Lemkul wrote:

On 3/13/18 10:32 AM, Alex wrote:
It appears that things have improved... I am just glancing and pullf and pullx data from the first sample config and both contain only one value, even though we set dim to 3D. Does this make sense?

I haven't used the 2018 pull code yet. Presumably this is correct, just the distance rather than all its components, though that would be a change from previous versions.




On 3/13/2018 8:18 AM, Justin Lemkul wrote:

On 3/13/18 10:17 AM, Alex wrote:
You may have a situation that requires manual assignment of pull_group1_pbcatom1, as the automatic choice of

Sorry, that should be pull_group1_pbcatom. Must remind myself not to email before coffee...

Did you mean pull_group2_pbcatom? In my case:

pull_group1_name        = K
pull_group2_name        = CNT

The language for 5.1 pull is (you be the judge on how clear it is):


   (0) The reference atom for the treatment of periodic boundary
   conditions inside the group (this has no effect on the treatment of
   the pbc between groups). This option is only important when the
   diameter of the pull group is larger than half the shortest box
   vector. For determining the COM, all atoms in the group are put at
   their periodic image which is closest topull-group1-pbcatom
<http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#mdp-pull-group1-pbcatom>.    A value of 0 means that the middle atom (number wise) is used. This
   parameter is not used withpull-group1-geometrycylinder. A value of
   -1 turns on cosine weighting, which is useful for a group of
   molecules in a periodic system,/e.g./a water slab (see Engin et al.
   J. Chem. Phys. B 2010).

Indeed, my group2 is a membrane that is wider than the shortest half-box. I am assuming it would be a single atom belonging to the pore region...

Yes, pull_group2_pbcatom, not 1.





Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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