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 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
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
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
Yes, pull_group2_pbcatom, not 1.
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