[gmx-users] distance calculation

[Mark Abraham]

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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>
>