[gmx-users] Calculate distance between two atoms

[Amjad Farooq]

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

Thank you very much for your help!
Amjad
 
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AMJAD FAROOQ PhD DIC
Associate Professor and Laboratory Head
Farooq Laboratory of Macromolecular Biophysics, Gautier Bldg #217/219
Dept of Biochemistry & Molecular Biology and USylvester Braman Family Breast Cancer Institute
Leonard Miller School of Medicine, University of Miami, Miami, FL 33136

1011 NW 15th Street #217, Miami, FL 33136 (Mailing Address)
a.farooq at miami.edu | amjad at farooqlab.net | amjadfarooq at yahoo.com
off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 
www.farooqlab.net 
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