[gmx-users] Pull parameters to Restrain motion along the Z Axis

Barnett, James W. jbarnet4 at tulane.edu
Thu Aug 27 15:13:33 CEST 2015


> suppose distance between center of masses of protein and DPPC is say
> 2.5 in
> the z direction and if pull_start =yes and pull_init is 1.0 then
> sampling
> will be at center of mass distance = 3.5 in only Z direction, since I
> have
> selected N N Y.

That's correct.

> 
> and if pull_start =No and pull_init is 1.0 then sampling will be done
> at
> center of mass distance = 1 in only Z direction.

That's correct.

> 
> Well,I am using that pull in each mdp file ( minimization,
> equilibration
> and Production). Is that a problem ?

That's fine.

> It remains nearly at the similar
> distance as 0th frame throughout the simulations in Z direction.

You may be near an energy barrier if you are sure that you have set the
pull settings correctly, so you might have to increase the "spring"
constant k in the pull code to get it exactly where you want it.


> I am sorry for the misunderstanding. I want to allow my protein only
> move
> in x, y direction. I am restricting it so It can't move be in Z
> direction.

There might be other ways to do that with restraints, but this may give
you the result you want, too.

> 
> On Wed, Aug 26, 2015 at 8:38 PM, Barnett, James W <
> jbarnet4 at tulane.edu>
> wrote:
> 
> > pull_start = yes means COM distance is added to the pull_init
> > value. So
> > whatever distance your two pull groups starts out at plus pull_init
> > is the
> > window where it will sample.
> > 
> > pull_start = no means just the pull_init value is used as the
> > reference
> > distance. If you have pull_init set to 1.0 then that is the
> > reference
> > distance for sampling (the window where it will sample).
> > 
> > If you haven't equilibrated at the reference distance it could take
> > a
> > little bit for your two groups to get to the reference distance. At
> > t=0
> > nothing has moved yet, unless you have equilibrated with the same
> > pull code
> > parameters already (and you probably should, depending on what your
> > goal is
> > here), so you should not expect the distance between the two groups
> > to
> > already be near the reference distance before the simulation has
> > begun.
> > 
> > If you're looking to restrain the protein's movement to the z-axis
> > such
> > that it can only move along the z-axis, this is not what you'll be
> > achieving. Here are you restricting the movement of the protein
> > along the
> > z-axis but it is free to move in the x and y directions. I may be
> > misunderstanding your goal here. There are some flat-bottom
> > restraints you
> > can add to make it such that the protein only moves in one
> > direction if
> > that's your goal. Check the relevant sections in the manual.
> > 
> > --
> > James “Wes” Barnett, Ph.D. Candidate
> > Louisiana Board of Regents Fellow
> > Chemical and Biomolecular Engineering
> > 
> > Tulane University
> > 341-B Lindy Boggs Center for Energy and Biotechnology
> > 6823 St. Charles Ave
> > New Orleans, Louisiana 70118-5674
> > jbarnet4 at tulane.edu
> > 
> > 
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> > Live King
> > <vikasdubey1008 at gmail.com>
> > Sent: Wednesday, August 26, 2015 5:25 AM
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] Pull parameters to Restrain motion along the Z
> > Axis
> > 
> > Hi,
> > 
> > I use Gromacs 4.5.5. I have these pull parameters which I use to
> > restrain
> > my Protein motion along the Z axis.I want to make sure these
> > parameters are
> > fine or not since , I am not getting expected results.
> > Also, please suggest any other parameters I can add.
> > 
> > ;Pull to restrain Z position
> > pull                     = umbrella
> > pull_geometry            = distance
> > ; Select components for the pull vector. default: Y Y Y
> > pull_dim                 = N N Y
> > pull_start               = No
> > pull_nstxout             = 10000
> > pull_nstfout             = 10000
> > pull_ngroups             = 1
> > pull_group0              = DPPC
> > pull_group1              = Protein
> > pull_vec1                = 0.0 0.0 0.0
> > pull_init1               = 1.0
> > pull_rate1               = 0
> > pull_k1                  = 1000
> > pull_kB1                 = 1000
> > 
> > 
> > Here I am completely confused in pull_init and pull_start. From my
> > understanding, pull_init is the reference distance at t=0. The
> > reference
> > distance is the distance between COM of the pull group and COM of
> > the
> > reference group.I have set my reference group as DPPC and pull
> > group as
> > Protein, which means my Z_distance should be Ideally ~ 1.00 if my
> > pull_start is set up as  "No" and should be ~0.0 if that is set it
> > as
> > "Yes".Since, pull_start means the initial COM distance is the
> > reference
> > distance for the first frame.
> > 
> >  But my values are instead after the production run:-
> > 
> >  with pull_init =1.0 and pull_start = "Yes"
> >      time              |d|                 dx
> > dy                 dz
> >    0.0000000    4.5361605    0.9850349    2.3691738    3.7407854
> > 
> >  with pull_init =1.0 and pull_start= "No"
> > 
> >    0.0000000    2.8222415    0.7867510    2.5469491   -0.9268878
> > 
> > 
> > my protein is nearly at the center of membrane of box size
> > 
> >  7.34147   7.34147   7.34147
> > 
> > If somebody can help me I will be grateful.
> > 
> > Thanks,
> > Vikas
> > --
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