[gmx-users] Gmx distance

rose rahmani rose.rhmn93 at gmail.com
Thu Nov 22 13:35:31 CET 2018

```To be clear, i put 30 similar AA around NT i want to know how the average
distance of group PROTEIN( consist of 30 AA ) varies during 100nS
simulation. As i see in .gro file this distance decreased. I mean at the
first moment i put them about 3nm far from Z axis of NT. THIS 3NM IS THE
MINIMUM LENGTH OF A LINE BETWEEN AA COM POINT AND Z AXIS OF NT, AS YOU CAN
IMAGINE THIS LINE IS PERPENDICULAR TO Z AXIS OF NT. this length is decrease
after 100nS. But what i can't understand is that when i analyze it by
g_dist( i select ZnS(NT) and Group Potein(=30 AA) in g_dist).. this is the
result!

Group     0 (         System) has 27831 elements
Group     1 (          Other) has   408 elements
Group     2 (            ZnS) has   408 elements
Group     3 (        Protein) has   720 elements
Group     4 (      Protein-H) has   390 elements
Group     5 (        C-alpha) has    30 elements
Group     6 (       Backbone) has    90 elements
Group     7 (      MainChain) has    90 elements
Group     8 (   MainChain+Cb) has   120 elements
Group     9 (    MainChain+H) has   180 elements
Group    10 (      SideChain) has   540 elements
Group    11 (    SideChain-H) has   300 elements
Group    12 (    Prot-Masses) has   720 elements
Group    13 (    non-Protein) has 27111 elements
Group    14 (          Water) has 26703 elements
Group    15 (            SOL) has 26703 elements
Group    16 (      non-Water) has  1128 elements

Select a group: 2
Selected 2: 'ZnS'
Select a group: 3
Selected 3: 'Protein'

0.0000000    0.2176011   -0.0120678   -0.0465498    0.2122209
1.0000000    0.2124534   -0.0301750   -0.0463870    0.2051198
2.0000000    0.1923753   -0.0158403   -0.0510135    0.1848106
3.0000000    0.1885315   -0.0107298   -0.0488160    0.1817856
4.0000000    0.2044982   -0.0052650   -0.0490329    0.1984630
5.0000000    0.2033602   -0.0002742   -0.0429537    0.1987720
6.0000000    0.2050487    0.0013833   -0.0444658    0.2001646
7.0000000    0.2002475    0.0041072   -0.0415003    0.1958568
8.0000000    0.2006473    0.0033450   -0.0511889    0.1939790
9.0000000    0.2032918   -0.0000119   -0.0330052    0.2005947
10.0000000    0.2255659    0.0003929   -0.0415857    0.2216990
11.0000000    0.2243811    0.0118313   -0.0344751    0.2214010
.
.
.
99990.0000000    0.6195676   -0.1357532   -0.0029635    0.6045051
99991.0000000    0.5355353   -0.3716600    0.0125020    0.3853707
99992.0000000    0.5243484   -0.3698001    0.0180452    0.3712997
99993.0000000    0.4459361   -0.1407223   -0.2021322    0.3717511
99994.0000000    0.5592619   -0.3545561   -0.2162843    0.3745463
99995.0000000    0.5707593   -0.3472078   -0.2309759    0.3896961
99996.0000000    0.5238984   -0.3467841   -0.0103419    0.3925600
99997.0000000    0.5122938   -0.3379052    0.0097873    0.3849275
99998.0000000    0.5608831   -0.3396225   -0.2052171    0.3963993
99999.0000000    0.5230988   -0.3479364    0.0172603    0.3902240
100000.0000000    0.5158455   -0.3283865    0.0047119    0.3977897

If the nanotube is along Z axis, so how g_dist calculate the COM of nano
tube? Is it each point along Z axis which pass center of nano tube or COM
in this case is just one point in the nanotube. If it is the second one, so
g_dist doesn't calculate perpendicular distance from AA to Z axis... so it
is completely different from what i want.

How can i get what i want?
this is exactly what want it is not an article it is just the figure 2
https://www.sciencedirect.com/science/article/pii/S0008622314006691#f0010

i'm completely confused!

Best
Rose

On Wed, 7 Nov 2018, 18:32 Justin Lemkul <jalemkul at vt.edu wrote:

>
>
> On 11/3/18 2:15 PM, rose rahmani wrote:
> > On Sat, 3 Nov 2018, 19:56 Justin Lemkul <jalemkul at vt.edu wrote:
> >
> >>
> >> On 11/2/18 11:36 AM, rose rahmani wrote:
> >>> but this is output of -oall. its not a single value?!
> >> You are asking in your command for all interatomic distances between the
> >> groups (presumably, because you haven't shown your selection). This
> >> command won't yield what you're hoping to see and my advice does not
> >> apply for this type of situation (which doesn't seem to even match your
> >> original statement of your problem).
> >>
> >>>     gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
> >>> # gmx distance is part of G R O M A C S:
> >>> #
> >>> #
> >>>
> >>
> Â¸<8d><9a><9a><91>ÃÂ­<9a><9b>ÃÂ°<8d><9e><91><98><9a>ÃÂ²<9e><98><9a><91><8b><9e>ÃÂ¾<85><8a><8d><9a>ÃÂ¼<86><9e><91>ÃÂ¬<94><86><9d><99a>8a><<
> >>> #
> >>> @    title "Distance"
> >>> @    xaxis  label "Time (ps)"
> >>> @    yaxis  label "Distance (nm)"
> >>> @TYPE xy
> >>>
> >>>       1.000    0.229    0.229    0.446    0.582    0.446    0.229
> 0.446
> >>> 0.583    0.447    0.229    0.447    0.227    0.228    0.229    0.446
> >>> 0.582    0.446    0.228    0.446    0.583    0.447    0.228    0.447
> >>> 0.227    0.227    0.228    0.446    0.582    0.446    0.227    0.446
> >>> 0.583    0.447    0.227    0.447    0.227    0.228    0.229    0.446
> >>> 0.582    0.446    0.228    0.446    0.583    0.447    0.228    0.447
> >>> 0.227    0.228    0.229    0.446    0.582    0.446    0.228    0.446
> >>> 0.583    0.447    0.228    0.447    0.227    0.229    0.229    0.446
> >>> 0.582    0.446    0.229    0.446    0.583    0.447    0.229    0.447
> >>> 0.227    0.229    0.229    0.446    0.582    0.446    0.229    0.446
> >>> 0.583    0.447    0.229    0.447    0.227    0.228    0.229    0.446
> >>> 0.582    0.446    0.228    0.446    0.583    0.447    0.228    0.447
> >>> 0.227    0.228    0.229    0.446    0.582    0.446    0.228    0.446
> >>> 0.583    0.447    0.228    0.447    0.227    0.227    0.228    0.446
> >>> 0.582    0.446    0.227    0.446    0.583    0.447    0.227    0.447
> >>> 0.227    0.228    0.229    0.446    0.582    0.446    0.228    0.446
> >>> 0.583    0.447    0.228    0.4
> >>> .
> >>> .
> >>> .
> >>>
> >>> and this is -o of g_dist;
> >>>    g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
> >>> #
> >>> # g_dist is part of G R O M A C S:
> >>> #
> >>> # GRowing Old MAkes el Chrono Sweat
> >>> #
> >>> @    title "Distance"
> >>> @    xaxis  label "Time (ps)"
> >>> @    yaxis  label "Distance (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 "|d|"
> >>> @ s1 legend "d\sx\N"
> >>> @ s2 legend "d\sy\N"
> >>> @ s3 legend "d\sz\N"
> >>>      0.0000000    0.2176011   -0.0120678   -0.0465498    0.2122209
> >>>      1.0000000    0.2124534   -0.0301750   -0.0463870    0.2051198
> >>>      2.0000000    0.1923753   -0.0158403   -0.0510135    0.1848106
> >>>      3.0000000    0.1885315   -0.0107298   -0.0488160    0.1817856
> >>>      4.0000000    0.2044982   -0.0052650   -0.0490329    0.1984630
> >>>      5.0000000    0.2033602   -0.0002742   -0.0429537    0.1987720
> >>>      6.0000000    0.2050487    0.0013833   -0.0444658    0.2001646
> >>>      7.0000000    0.2002475    0.0041072   -0.0415003    0.1958568
> >>>      8.0000000    0.2006473    0.0033450   -0.0511889    0.1939790
> >>>      9.0000000    0.2032918   -0.0000119   -0.0330052    0.2005947
> >>>     10.0000000    0.2255659    0.0003929   -0.0415857    0.2216990
> >>>     11.0000000    0.2243811    0.0118313   -0.0344751    0.2214010
> >>>     12.0000000    0.2347855    0.0078275   -0.0383532    0.2314994
> >>>     13.0000000    0.2371541    0.0081918   -0.0388267    0.2338107
> >> Here, you have what you want (I assume), and the first column after the
> >> time is all you need. It's the distance, which also can't be negative
> >> because it is the magnitude of the vector length and is unsigned.
> >>
> > How S0 is calculated? Does it resulted from distance between COM of amino
> > acid and COM of tube? Although, it is the magnitude of ... but it's
>
> The distance you get is the distance you ask for in your selection
> (which isn't shown or stated). The distance formula is quite simple,
> consult any geometry textbook.
>
> > calculated from x,y,z which may be negative and were not abaolute?! In
> > addition, i put AAs (more than) 1.5 nm far from tube as an initial
> > configuration, but any 1.5 nm distance..???
> >
>
> A component of a vector may be positive or negative, these are just
> differences along x, y, and z. The total length of a vector is a
> magnitude and is therefore positive.
>
> -Justin
>
> >
> >> -Justin
> >>
> >>> .
> >>> .
> >>> .
> >>>
> >>>
> >>> On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >>>
> >>>> On 11/1/18 2:25 PM, rose rahmani wrote:
> >>>>> I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
> >>>>> multiplied by (-), but how should i modify second column,i don't know
> >> how
> >>>>> s0 is calculated by g_distance to modify it??
> >>>> The output of -oall is a single value, the actual distance, which I
> >>>> assume is what you are talking about in your previous message. You can
> >>>> parse that column in any scripting language you like and
> >>>>
> >>>> [ pseudocode, not functional ]
> >>>> if (value < 0)
> >>>> {
> >>>>        value *= -1
> >>>> }
> >>>>
> >>>> -Justin
> >>>>> On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >>>>>
> >>>>>> On 10/31/18 12:06 PM, rose rahmani wrote:
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> I want to calculate distances between fixed tube in the middle of
> the
> >>>> box
> >>>>>>> and amino acids(all are same type)around it. But gmx distance gives
> >> me
> >>>>>> the
> >>>>>>> relative distance i mean AA can be front or back( can be 0.5 or
> -0.5
> >>>> from
> >>>>>>> tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have
> >> the
> >>>>>>> absolute value of distances?
> >>>>>> Write a simple post-processing script that multiplies any negative
> >> value
> >>>>>> by -1.
> >>>>>>
> >>>>>> -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.thelemkullab.com
> >>>>>>
> >>>>>> ==================================================
> >>>>>>
> >>>>>> --
> >>>>>> Gromacs Users mailing list
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> >>>>>> posting!
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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.thelemkullab.com
> >>>>
> >>>> ==================================================
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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.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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> >> send a mail to gmx-users-request at gromacs.org.
>
> --
> ==================================================
>
> 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.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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```