[gmx-users] regarding g_rdf

[soumadwip ghosh]

Dear all,
              I am willing to calculate the rdf of certain cations from
different group of molecules in the system. For example, I have got a DNA
backbone (having P, O1P and O2P atoms), DNA major groove (having all the
atoms a guanine and cytosine residue can have together) and a minor groove
(having all the atoms an adenine and thymine residue can have together).
Now I want to calculate g_rdf between Na/ backbone, Na/minor and Na/major.
Should I proceed with the -com option or not? I am not understanding the
concept of -rdf option for selecting between geometry/molecules.


Please help me out.


Thanks and regards,
Soumadwip Ghosh
Research fellow,
Indian Institute Of Technology, Bombay,
India.