So, then, it's what I said. In any case, I must say that the probe along
Z was more representative of the reality: a hemispherical slice probes a
circle near the surface of the membrane, which has nothing to do with
the pore, but naturally produces a barrier. I wish there was a way to
probe a spherical symmetry within a given solid angle. If pullf/pullx
data had any angular info, we could script our own implementation of
WHAM, but alas.
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
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
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
their periodic image which is closest topull-group1-pbcatom
A value of 0 means that the middle atom (number wise) is used.
parameter is not used withpull-group1-geometrycylinder. A
-1 turns on cosine weighting, which is useful for a group of
molecules in a periodic system,/e.g./a water slab (see Engin
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.
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