[gmx-users] Regarding rdf and number of molecules in the FSS of tetramer

[Ashma Khan]

Dear user's
I have calculated the rdf of urea molecules around the peptides for
different concentration of urea and obtained that peak height of first
solvation shell (FSS) decreases with increase in concentration of urea.
After that I have calculated the number of urea molecules in FSS and found
that urea molecules in the FSS increases with concentration of urea. There
is no correlation between the peak height of FSS and number of urea
molecules. Can anybody suggest me ? what is the reason
The command I have used is
gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com -seltype
whole_res_com
gmx select -f md.xtc -s md.tpr -os number.xvg -select "resname URE and
within 0.5 of group protein" -selrpos whole_res_com -seltype whole_res_com


-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh