# [gmx-users] gmx distance

Justin Lemkul jalemkul at vt.edu
Wed Jan 31 18:44:21 CET 2018

```
On 1/31/18 12:41 PM, Nick Johans wrote:
> 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;
> |
> |
> |<---------(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?

You're applying a restraint only along z. The protein is free to move in
x and y, and it has done just that. The total COM distance is produced
by gmx distance, but again, the z-component of this vector is in
agreement with what is in pullx.xvg, which is dZ, e.g. the z-component
of the distance. This is the only quantity that matters.

-Justin

> 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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--
==================================================

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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