[gmx-users] Calculate distance between two atoms

[Justin A. Lemkul]

Amjad Farooq wrote:
> Hello everyone,
> 
> I would like to calculate distance between two atoms from an MD run. For 
> example, how do I probe changes in distance between CD atom of Pro23 and 
> OE1 atom of Glu75 as a function of simulation time.
> 
>  From the manual, I understand that one should use the command g_dist 
> that includes the index.ndx file. My questions are:
> 
> (1) How do I create an index.ndx file for the the above-mentioned pair 
> of atoms?

Use make_ndx.  Type 'help' at the prompt for examples.  For indices with just 
one atom each this is not strictly necessary; you can create the necessary 
groups with a text editor.

> (2) What is the exact format of g_dist that should be applied on the 
> command line?
> 

Please read g_dist -h.

-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

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