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

[Live King]

Hi James,

Thanks for your reply. I roughly got your point and still kinda confused.
Please let me know If I am wrong .

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.

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.


Well,I am using that pull in each mdp file ( minimization, equilibration
and Production). Is that a problem ? It remains nearly at the similar
distance as 0th frame throughout the simulations in Z direction.

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.


Thanks,
Vikas




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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