On 10/8/18 3:22 AM, Rakesh Mishra wrote:
Dear Dr. Justin
Thanks for your patience to reply me. I think for last 3-4 months
we are discussing about the pulling. I agreed with your statement to
[stop thinking concretely in terms of a "reference" and a
"pulled" group ]. I am also not thinking in terms of this nomenclature.
I just thought as a end coordinate of bias. I checked many combination
for pulling two groups in opposite direction. Now I am getting fine to
pull groups
by applying two bias potential. like..
; Pull code
pull = yes
pull_ngroups = 4
pull_ncoords = 2
pull_group1_name = r_24
pull_group2_name = r_12
pull_group3_name = r_24
pull_group4_name = r_12
; definition of reaction coordinate 1, group 1-2
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_groups = 1 2
pull_coord1_dim = Y N N
pull_coord1_rate = 0.005 ; 0.005 nm per ps = 5nm per 1 ns
pull_coord1_k = 500 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance >
0
; definition of reaction coordinate 2, group 3-4
pull_coord2_type = umbrella ; harmonic biasing force
pull_coord2_geometry = distance ; simple distance increase
pull_coord2_groups = 3 4
pull_coord2_dim = Y N N
pull_coord2_rate = 0.005 ; 0.005 nm per ps = 5nm per 1
ns
pull_coord2_k = 500 ; kJ mol^-1 nm^-2
pull_coord2_start = yes ; define initial COM distance
0
In this way I am getting conceptually correct output. Now there is no
changes
of out put value of force-time by changing the saving frequency of
co-ordinates of
position , energy etc, which I was getting previously.
now my request is that please check above pull protocol. lastly in this
discussion
I have two query.
1- Reaction coordinate means what ? . In my view its position coordinate.
Google is your friend.
i.e end to
end distance between two groups during pulling or something else.
2- Here in above protocol,
pull_coord1_dim = Y N N
pull_coord1_dim = Y N N
this is showing that groups are pulling in x direction and not in Y
and Z direction.
so what will be the need to define
pull_coord1_vec = 1 0 0
pull_coord2_vec = 1 0 0 .
The different geometry specifications have different requirements. The
"distance" method requires Y/N, whereas the "direction" method requires
a vector.
-Justin
I think both are presenting the same thing.
Hoping your previous views on my these query. I think after that I will
have almost
negligible doubts regarding pulling.
And one another thing is that, If we want to change the pulling protocol
like to apply
force as piconewton/ps then in algorithm of gromacs, where we need to
implement in installed
gromacs in our machine.
On Fri, Oct 5, 2018 at 7:10 PM Justin Lemkul <jalem...@vt.edu> wrote:
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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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
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Blacksburg, VA 24061
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http://www.thelemkullab.com
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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
http://www.thelemkullab.com
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==================================================
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
http://www.thelemkullab.com
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