From: Axel Kohlmeyer (
Date: Tue Apr 11 2017 - 09:54:28 CDT

On Tue, Apr 11, 2017 at 5:06 AM, Jeams Anderson <>

> 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.

​it is impossible to know without more detailed information what your
system is and what you are comparing your results to. it sounds, like you
want to compute a density profile and not a g(r).​ radial distribution
functions between atoms of a surface and a liquid are of limited value,
since - unlike in the bulk case - they are dependent on the orientation of
the system and the position of the liquid atoms in space relative to the

> 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.

yes. you are confusing two different properties: ​RMSD (root mean squared
deviation from reference) != MSD​ (mean squared displacement)


> 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

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.