VMD-L Mailing List

From: parinaz bashirbanaem (parinaz.bashirbanaem_at_gmail.com)
Date: Fri Feb 19 2021 - 10:46:32 CST

Hi all,

I am running MD simulation (NAMD package) for the DNA-RNA complex. I want
to calculate RDF by VMD, I have opened my trajectory by loading *.pdb file
and *.dcd file. For the calculation of the RDF, in the *selection-1
*section I have selected “nucleic and resid 51 and index 1598” and
for selection-2
section I have selected “resname SOD”. However, I am not sure that my
process is right or not because the result is a bit anomalous from the
reference one.

 Thank you very much for any suggestion.

 Best regards,

 Parinaz.

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