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.
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 .
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
> >>
> >> --
> >> ==================================================
> >>
> >> 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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--
*With Best-Rakesh Kumar Mishra*
* (RA)CSD SINP Kolkata, India*
*E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> *
*Phone n. +91 9473662491, +918777496532*
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