[gmx-users] Exactly same rdfs for different residues of protein with water

Apramita Chand apramita.chand at gmail.com
Sat Dec 17 16:05:28 CET 2016

Dear All,
 I'm trying to see how the rdf varies for a particular interaction (peptide
carbonyl oxygen with hydrogen of water) across different residues. I chose
the oxygen atoms belonging to different residues in the index file and also
chose the hydrogen atoms from water. To my surprise, all the rdfs for
different residues are exactly coinciding with each other. I checked with
both corrected and uncorrected trajectory files. Also, I checked with
another simulation, where I've made a binary mixture. In that simulation,
this particular interaction again coincides exactly . When I plot both
files from these two simulations , two different plots (corresponding to
all coincided rdfs from different residues for each simulation) are seen.
Can anyone please explain this anomaly?


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