[gmx-users] Gmx distance

rose rahmani rose.rhmn93 at gmail.com
Sat Nov 3 19:15:30 CET 2018 

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:
> > #
> > #
> >
> ¸<8d><9a><9a><91>í<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<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
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..???



> -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?
> >>>>> Would you please help me?
> >>>> 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
> >>
> >> ==================================================
> >>
> >> --
> >> 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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>
> --
> ==================================================
>
> 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!
>
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