# [gmx-users] pulling in opposite direction

Rakesh Mishra rockinbhu at gmail.com
Fri Oct 12 09:27:10 CEST 2018

```Dear Justin .

Thanks for your response. And yes of course google is  best friend for all.

"distance" method requires Y/N, whereas the "direction" method requires
a vector."
But , "direction" method (where vector needs to define ) also gives the
same result
as we obtain the result in case of  geometry define as "distance" (where we
do not define vector).

Just please tell me  (in case of pull_geometry = direction) , what is the
difference between
following below two conditions.

pull_coord1_vec             = 1 0 0
pull_coord1_dim             = Y N N
&
pull_coord1_vec             = 1 0 0
pull_coord1_dim             = N N Y

and vector can be 0/1 or may be decimal number like 0.2 , 0.5 3tc.

On Wed, Oct 10, 2018 at 5:54 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
>
> > 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 <jalemkul at 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 <jalemkul at 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
> >> 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
> >>>>
> >>>> jalemkul at vt.edu | (540) 231-3129
> >>>> http://www.thelemkullab.com
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> posting!
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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
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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>

--

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +918777496532*
```