[gmx-users] Pulling two groups in opposite direction

[Naba]

>
> On 5/17/18 1:39 AM, Naba wrote:
> >> On 5/16/18 3:32 AM, Naba wrote:
> >>> Dear all,
> >>>
> >>> I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> >>> acids from its homodimer in opposite directions along z axis. The
> >>> interfaces of each protein chain is parallel to the z axis. I do not
> need
> >>> any restraints in this case. I have gone through the GROMACS manual and
> >>> some of the previous archived messages and set the following mdp
> options.
> >>>
> >>> ; Pull code
> >>> pull                    = yes
> >>> pull_ngroups            = 2
> >>> pull_ncoords            = 2
> >>> pull_group1_name        = chain_A
> >>> pull_group2_name        = chain_B
> >>> ;pull_group3_name = Protein
> >>> pull_coord1_type = umbrella
> >>> pull_coord2_type = umbrella
> >>> pull_coord1_init = 0.0
> >>> pull_coord2_init = 0.0
> >>> pull_coord1_start = yes           ; define initial COM distance > 0
> >>> pull_coord2_start = yes
> >>> pull_coord1_geometry    = direction
> >>> pull_coord2_geometry    = direction
> >>> pull_coord1_groups      = 2 1
> >>> pull_coord2_groups      = 1 2
> >>> pull_coord1_dim         = N N Y
> >>> pull_coord2_dim         = N N Y
> >> Note that pull_coord*_dim is not relevant when using "direction"
> geometry.
> >>
> >>> pull_coord1_rate        = 0.01        ; 0.008 nm per ps = 8 nm per ns
> >>> pull_coord2_rate        = 0.01         ; 0.008 nm per ps = 8 nm per ns
> >>> pull_coord1_k           = 2000          ; kJ mol^-1 nm^-2
> >>> pull_coord2_k           = 2000
> >>> pull_coord1_vec        = 0.0 0.0 1.0
> >>> pull_coord2_vec        = 0.0 0.0 -1.0
> >>> nstcalcenergy = 1
> >>> nhchainlength = 1
> >>>
> >>> But it fails to pull chain_A in positive z direction. However, chain_B
> is
> >>> seemed to pull in negative z direction. Someone please suggest the
> proper
> >>> way to pull two groups in opposite directions, or if there is anything
> >> that
> >>> I am missing.
> >> What is the point of pulling in two directions? Separation of two
> >> species requires only one reaction coordinate. For every action, there
> >> is an equal, but opposite reaction...
> >>
> >> -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
> >>
> >> ==================================================
> >
> >
> > Thank you Dr. Justin.
> > Besides PMF calculations during umbrella sampling, I want to observe the
> > interacting residues while pulling both the chain in opposite directions.
> > In your tutorial you pulled only one chain for your specific case.
> Whereas
> > in my case, the point to be observed how smoothly or rigorously the
> chains
> > are interacting with their residues in interface due to the application
> of
> > two equal forces in opposite directions.
> >
> > Anyways, from your reply should I understand that pulling only one chain
> > without any restraints in only one direction will do my job? Please
> correct
> > me the mdp settings.
>
> Do not pull along only one dimension. A normal, soluble protein complex
> will rotate in space so you should pull in all three dimensions. There
> are several ways to accomplish this pulling, but indeed you only need
> one reaction coordinate to induce separation.
>
> -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
>
> ==================================================
>
> Thank you again Dr. Justin.

How do I pull only chain so that both the chains should show sliding
movement  with respect to one another?

For your convenience here is the picture of the homodimer I am dealing
with: https://www.dropbox.com/s/6yh5vo3jcieh7rm/dummy.png?dl=0 . I want to
pull the chains in the direction with the arrow marks given there in the
picture.

More precisely, it is N-terminal part of a very huge insoluble protein
reported to be in dimeric form. However, comm-mode = Linear showed me
unexpected rotation at very beginning of the run which entirely disturbed
the initial orientation of the molecule along z axis. In contrast,
comm-mode = Angular and pull_coord1_dim = Y Y Y with pull_ncoords = 1
partially fulfilled my purpose but not in that way as I want both chains to
be slide over one another.

Hope you will make me more clear about all these.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India