[gmx-users] Temperature variation of CHARMM force field

soumadwip ghosh soumadwipghosh at gmail.com
Sat Jul 4 16:31:15 CEST 2015

Thanks Justin for your help as always

I have calculated the RDF between DNA atoms (O2 which is a part of DNA
major groove and the P atom of the phosphate backbone of the DNA) and
water Oxygen atoms separately snd fro the plot it is evident that the
solvation structure around these two atoms are not purturbed
significantly at different temperatures under study. If I am right
g(r) is a function of temperature right? Where I have shown that the
DNA ion interaction at different temperature is different from PMFs
which I calculated using g(r) between specific atoms situated on DNA
binding ites and that of some molecular ions and then the temperature
dependent PMFs have been decoposed to obtain the thermodynamic
contribution facilitating each DNA site specific ion binding
processes, please help me understand why the RDF for sovent atoms with
some DNA atoms are not getting altered significantly on changing

Nevertheless, do you think that showing the alomost overlapping RDFs
of DNA_O vs OW and DNA_P vs OW would proove a point to my reviewer
that the chosen force field just works fine within the range of  the
simulation temperature chosen for this study (T= 300 +_ 30K)?
Thanks for your help in advance

Soumadwip Ghosh
Research Fellow

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