# [gmx-users] gmx distance

Nick Johans johans.nick93 at gmail.com
Wed Jan 31 18:41:20 CET 2018

```Sorry, i think there is sth, maybe i've learnt wrong. let me draw it ;)
| = ZnS SHEET     and    @=Protein

conf0.gro

|
|
|<------------(Z)distance=1.76----------->@
t=0
|
|

next time if dZ=0.5 so;
|
|
|<---------(Z)distance=1.26-------->@
t=t1
|
|

next time if dZ=0.8 so;
|
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|<---------(Z)distance=0.96-------->@
t=t2
|
|

I want to tell you this is my last conf.gro

|
|
|
|
|<dist~=0nm>@                                                          t=tn

so WHY it shows me 1.611?how can i proof and calculate this distance?ok
they are not coincident because i have sheet(which interact by it's
surface) and Protein, but why it should be important? because the sheet is
freez and immobile and i just want Z distance. and this distance should be
the absolute distance between 2 point( difference between z=4.287and COM of
protein in each frame). this is all my imagination. What i have
misunderstand?

best regards

On Wed, Jan 31, 2018 at 8:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/31/18 11:22 AM, rose rahmani wrote:
>
>> Hi,
>> This is md_pull.mdp
>>
>> integrator               = md
>> dt                       = 0.001
>> nsteps                   = 4000000
>> nstxout                  = 1000
>> nstvout                  = 1000
>> nstfout                  = 500
>> nstlog                   = 500
>> nstenergy                = 500
>> nstxtcout                = 500
>> nstlist                  = 10
>> rlist                    = 1.5
>> coulombtype              = pme
>> rcoulomb                 = 1.5
>> vdwtype                  = Switch
>> rvdw_switch              = 1.0
>> rvdw                     = 1.2
>> pcoupl                   = no
>> gen_vel                  = no
>> constraints              = h-bonds
>> ns_type                  = grid
>> pbc                      = xy
>> freezegrps               = WAL ZnS
>> freezedim                = Y Y Y Y Y Y
>> energygrp-excl           = WAL WAL ZnS ZnS
>> energygrps               = SOL WAL ZnS Protein NA CL
>> nwall                    = 2
>> wall-atomtype            = C C
>> wall-type                = 9-3
>> wall-density             = 150 150
>> wall-ewald-zfac          = 3
>> ewald-geometry           = 3dc
>> fourierspacing           = 0.12
>> tcoupl                   = v-rescale
>> tc-grps                  = System
>> tau-t                    = 0.1
>> ref-t                    = 300
>>
>> ; Pull code
>> pull                    = umbrella
>> pull_ngroups            = 1
>> pull_group0             = ZnS
>> pull_group1             = Protein
>> pull_geometry           = distance
>> pull_dim                = N N Y
>> pull_rate1              = -0.01
>> pull_k1                 = 5000
>> pull_start              = yes
>> pull_nstxout            = 50
>> -------------------------------------------
>> pullx.xvg;
>>
>> @    title "Pull COM"
>> @    xaxis  label "Time (ps)"
>> @    yaxis  label "Position (nm)"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "0 Z"
>> @ s1 legend "1 dZ"
>> 0.0000  4.287   1.76284
>> 0.0500  4.287   1.75329
>> 0.1000  4.287   1.74622
>> 0.1500  4.287   1.73983
>> 0.2000  4.287   1.73664
>> 0.2500  4.287   1.7377
>> .
>> .
>>
>> 3999.7500       4.287   0.258632
>> 3999.8000       4.287   0.258738
>> 3999.8500       4.287   0.258955
>> 3999.9000       4.287   0.260093
>> 3999.9500       4.287   0.25843
>> 4000.0000       4.287   0.258025
>> -------------------------
>> Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
>> whole
>> Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg
>>
>> this is distwhole.xvg
>>     0.0000000    1.7630774    0.0185155   -0.0197599   -1.7628694
>>     0.5000000    1.7529889   -0.0133090    0.0135729   -1.7528858
>>     1.0000000    1.7453604   -0.0344692    0.0751038   -1.7434030
>>     1.5000000    1.7691813   -0.0621567    0.0087628   -1.7680674
>> .
>> .
>> 3997.5000000    1.6120006    0.9964043   -1.2400901   -0.2605782
>> 3998.0000000    1.6122891    0.9971979   -1.2404475   -0.2576084
>> 3998.5000000    1.6124574    0.9966092   -1.2406733   -0.2598433
>> 3999.0000000    1.6115565    0.9968075   -1.2396555   -0.2583475
>> 3999.5000000    1.6120616    0.9964568   -1.2404943   -0.2588253
>> 4000.0000000    1.6116294    0.9952377   -1.2410750   -0.2580390
>>
>> as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
>> group (Protein and ZnS sheet) in last frame are too close to each other.
>> so
>> why i see 1.611 in distwhole.xvg?
>>
>> and could you please tell me what is the relevance of pullx.xvg to g_dist
>> output?as you see pullx.xvg ensure that distance between 2 group is
>> decreasing, so...?
>>
>> is there anything i did not consider?
>>
>
> Your output is completely consistent. You're applying a biasing potential
> along the z-dimension only, so that's the only distance that mdrun cares
> about in establishing the reaction coordinate. The pullx.xvg file contains
> the COM coordinate of the "reference" group (group0) and in your case is
> just the z-coordinate, so that's the first data column. The second data
> column (dZ) is the displacement along the z-axis. Your COM distance results
> confirm this - your protein and ZnS are not exactly coincident; they have
> different x and y coordinates. But the z column in the distance output
> agrees with the pullx.xvg file (when considering the absolute value).
>
> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
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```