[gmx-users] g_dist output
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 9 14:46:11 CET 2010
John Shultz wrote:
> How come time is always 0.0000000
You're analyzing a .gro file, so there is no time information stored. If you
analyze a trajectory (i.e., .xtc or .trr), then the time is saved in the
> On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> John Shultz wrote:
>>> I am seeking clarification on what this output means. I believe it
>>> says that the x axis is divided into 4 time intervals and they are
>>> plotted against a y axis that measures total distance along all 3
>>> dimensional coordinates.
>>> Am I reading this correctly?
>> There should be no decomposition of time intervals here. Distance is
>> plotted continuously as a function of time. The first column is time, then
>> the total distance, then each of the x, y, and z components of that
>>> # This file was created Sat Jan 30 00:20:03 2010
>>> # by the following command:
>>> # g_dist -f md.gro -s md.tpr -n index.ndx
>>> # g_dist is part of G R O M A C S:
>>> # Glycine aRginine prOline Methionine Alanine Cystine Serine
>>> @ 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 0.0619448 0.0583303 0.0099401 -0.0183282
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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