[gmx-users] distance calculation

[tarak karmakar]

Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f  traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could not able to find the way how to specify the indices of the
two desired atoms.
( suppose I want to plot the distance between atom no. 500 (protein
backbone) and atom no. 879 (ligand atom) with respect to time)




On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 20/09/2012 2:05 PM, tarak karmakar wrote:
>>
>> Thanks Justin.
>>
>> But in my case I want to plot the distance between one  atom in the
>> backbone of the protein and other atom present in the ligand. Then how
>> can I specify these two atoms I need for plotting the distance between
>> them.
>
>
> g_dist treats the system as a list of atoms, and is ignorant of details like
> molecules. So you just need to tell it which atoms via their indices.
>
> Mark
>
>
>> On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>> On 9/19/12 2:55 PM, tarak karmakar wrote:
>>>>
>>>> Dear All,
>>>>
>>>> I want to calculate the distance between the nitrogen atom present in
>>>> the ligand and the H- attached to the backbone of the protein along a
>>>> long trajectory. So can anyone suggest me how to consider these two
>>>> atoms to calculate and plot the distance along with the time ?
>>>>
>>> g_dist with appropriate index groups.
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> 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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>>
>>
>>
>
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-- 
Tarak