[gmx-users] Gmx distance

rose rahmani rose.rhmn93 at gmail.com
Fri Nov 2 16:36:50 CET 2018 

but this is output of -oall. its not a single value?!

  gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
# gmx distance is part of G R O M A C S:
#
#
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#
@    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
.
.
.


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