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
--
========================================
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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