[gmx-users] distance calculation

[Mark Abraham]

On 20/09/2012 4:21 PM, tarak karmakar wrote:
> 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)

See manual 8.1 for discussion, and 
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx for more.

Mark

> 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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>