<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:10pt"><div>Hello everyone,</div><div><br></div><div>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.</div><div><br></div><div>From the manual, I understand that one should use the command g_dist that includes the index.ndx file. My questions are:</div><div><br></div><div>(1) How do I create an index.ndx file for the the above-mentioned pair of atoms?</div><div>(2) What is the exact format of g_dist that should be applied on the command line?</div><div><br></div><div>Thank you very much for your help!</div><div>Amjad<br></div> <div>************************************************************************************************************************************<br><span
style="font-weight:bold;">AMJAD FAROOQ PhD DIC</span><br>Associate Professor and Laboratory Head<br>Farooq Laboratory of Macromolecular Biophysics, Gautier Bldg #217/219<br>Dept of Biochemistry & Molecular Biology and USylvester Braman Family Breast Cancer Institute<br>Leonard Miller School of Medicine, University of Miami, Miami, FL 33136<br><span style="font-weight:bold;"><br></span>1011 NW 15th Street #217, Miami, FL 33136 (Mailing Address)<span style="font-weight:bold;"><br></span>a.farooq@miami.edu | amjad@farooqlab.net | amjadfarooq@yahoo.com<span style="font-weight:bold;"></span><span style="font-weight:bold;"> <br></span>off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 <span style="font-weight:bold;"><br></span>www.farooqlab.net <br>************************************************************************************************************************************</div> </div></body></html>