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

Barnett, James W jbarnet4 at tulane.edu
Wed Aug 26 17:08:09 CEST 2015

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


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.

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