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

Mark Abraham mark.j.abraham at gmail.com
Sat Dec 17 23:17:25 CET 2016


If "exactly coinciding" means the same numbers are computed in the .xvg
file, then you probably are just computing the same thing each time -
double check your index groups and command-line choices. If you mean that
they just look the same, then that could be a fair result if your protein
is small - you only expect differences at very short ranges, after all.


On Sun, Dec 18, 2016 at 2:05 AM Apramita Chand <apramita.chand at gmail.com>

> 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?
> Regards,
> Apramita
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