On 10/5/18 12:47 AM, Rakesh Mishra wrote:
Dear Justin thanks for ur reply.
Which means in this case,both group will act as a reference group for each
other.
Then now my question is, why without using two biasing potential, in case
of using one
biasing potential for two group, If I do not constrained reference group
then it automatically
move in the opposite direction w.r.t pulling group.
I feel like I've already explained how all of this works. The bias is
applied to the specified groups, and they evolve however they're going
to under the influence of the applied force.
It may help to stop thinking concretely in terms of a "reference" and a
"pulled" group. That's a conceptual convention that is actually somewhat
outdated now that GROMACS supports multiple, simultaneous biasing
potentials. Each group defines the end of a reaction coordinate. Their
relative positions matter in terms of defining the direction of the
bias, hence the "reference" and "pulled" nomenclature. But again, I
think that by enforcing such nomenclature, it's a bit misleading.
-Justin
On Thu, Oct 4, 2018 at 6:48 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 10/4/18 3:09 AM, Rakesh Mishra wrote:
Dear all.
How it is possible to pull reference group as well as pull group using
gromacs protocol simultaneously in opposite direction using umbrella
protocol
of pulling. So far non of the Gromacs expertise have given the answer of
this question. Hoping from response
If you want to pull two things in opposite directions, you need two
biasing potentials.
-Justin
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303 Engel Hall
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Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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