[gmx-users] g_dist output

[Justin A. Lemkul]

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 
individual frames.

-Justin

> On Tue, Mar 9, 2010 at 8:16 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> John Shultz wrote:
>>> Hello,
>>>
>>> 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
>> distance.
>>
>> -Justin
>>
>>> # 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
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 
> 

-- 
========================================

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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================