VMD-L Mailing List

From: Jeams Anderson (anddersonnyc_at_gmail.com)
Date: Tue Apr 11 2017 - 04:06:48 CDT

Hi all

I want to calculate RDF and RMSD by VMD. I am a Lammps user and I have
opened my trajectory by loading *.data file and *.dcd file.

For the calculation of the RDF, in the *selection-1 *section I have
selected my surface index which will be in Zero position in the selection-2
section I have selected the electrolytes index which is changing the
position. and I want to calculate the RDF of the electrolyte from the
surface. However, I am not sure that my process is right or not because the
result is bit anomalous from the reference one.

Regarding to the RMSD calculation, I want to observe the displacement of
the electrolyte on the surface. I have selected the index for electrolytes
and calculate the RMSD plot, But I am not sure that he procedure is OK or
not. Therefore I suppose might be I made some mistake in the procedure.

Could any one mention me any details tutorial or reference for the
calculation of the RDF and MSD by VMD or make some valuable comments

Thanks in advance

Anderson

University of Houston