Vitaly Chaban wrote:
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my
system.
To do this how should I define my index groups. Should I include all 125
molecuels in index file? now I have only the first 20 atoms (first
molecule)..
To get the total interaction energy among your hexanes, all atoms of
all C6H14's should be listed in the NDX file, e.g. 125 * 20...
The underlying issue with this approach is that there are then in excess of
125*125 energy terms written to the .edr file, which will quickly make this file
very (perhaps prohibitively) large. Let the OP be warned...
-Justin
Good luck.
Dr. Vitaly Chaban
--
========================================
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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