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

Live King vikasdubey1008 at gmail.com
Wed Aug 26 12:25:56 CEST 2015


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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