[gmx-users] distance calculation

[tarak karmakar]

thanks a lot Mark

On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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>>>>
>>>>
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>>
>
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-- 
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809