[gmx-users] Regarding RDF

Ashma Khan ashmakhan200 at gmail.com
Sat Sep 28 05:36:39 CEST 2019

Dear all,
I have calculated the rdf of urea molecules with different concentrations
along the peptide and obtained the result that in first solvation shell at
0.5 nm g(r) value decreases with increase in concentration but when I
calculated the number of urea molecules by gmx select at 0.5 nm, it
increases with concentration.Is it possible. Anybody can help me why this
is happening . I have used this command for calculating urea molecules and
averaged over the frames.
gmx select -f .xtc -s .tpr  -select 'resname URE and within 0.5 of group
potein' -os .xvg
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh

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