Re: radial distribution function

Date: Wed Mar 01 2006 - 08:25:45 CST


When the RDF.tcl scripts is run (open a Tk Console from the Extensions Menu, go
to the folder where the script is and type: source RDF.tcl), a tk window appears
on screen. It has the following options:

Total frames is the total number of frames once you've loaded the .psf and the
.dcd file in VMD. Don't load the RDF.tcl script before all the .dcd file frames
are loaded. On doing so, the RDF script won't consider all the frames in de .dcd.

Frames: start/end/skip. Is the set of frames from the .dcd file that will be
taken in account for the RDF calculations. start is the first; end is the last;
To take in account all the frames, skip is 1. To take every other frame, skip is
2, and so on. Tipically, the .dcd includes frames for minimization and
simulation. In that case, you can put only the frames related to [part of] the

from atom/to atom: The RDF is calculated taking in account the number of certain
atoms ("to atom") respect to another specific atom ("from atom").
segname, resname and name can be taken from the VMD Graphical Representations

Cutoff/mbin: Those define the cutoff(maximum) radial distance that'll be taken
in account for RDF calculations, and the number of bins(output points). If, for
instance cutoff is 15 and mbins 150, you'll get RDF points every 0.1A along the
radial 15A from the atom specified in the previous section. In other words:


Size of the box: RDF is a function said to give an insight on the local
structure in a molecule. However, it's tipically used in solvation studies. The
box size is refered to water(in my case) box. You can calculate that from VMD,
or take it from the .xsc NAMD file.

Press Run RDF. You should see in the Tk Console the calculations for each frame.
After all the calculations (It may take several minutes, few hours depending on
the computers, size of the system) you'll see the list of results(list of points).

After making the calculations you can save the results typing the name of the
file and then "Save".

Example. Thus, lets say that you want to calculate the RDF for a Carbon atom in
a molecule sourrounded by water molecules. The parameters could be:

Total frames: 10100 (100 for minimization, 10000 of simulation)
start: 101; end: 10099 (I've had problems in putting 10100. 1 frame in 10000
won't matter anyway); skip:1. (I'm taking all the frames related only to the

>From atom
Segname:BPTI; Resname:BTPI; Name: C10
To atom
Segname:WT1; Resname:TIP3; Name: H1 H2 OH2

Cutoff: 15
mbins: 150

x: 37.65; y: 37.65; z: 37.65

The colons are just to separate the title from typed characters. Don't type them
in the tk window of RDF.tcl. If you open the RDF.tcl in a text editor, you'll
see some of this information.
Hope this qualifies for a manpage of the RDF.tcl script!

Good luck!
Gonzalo Riadi.
Center for Bioinformatics and Molecular Simulations
University of Talca, Chile.

Mensaje citado por

> I try to use RDF.tcl script in vmd console but I don't understand all
> options in main window RDF's. I would like to ask All about some
> description or manual for this script, or any program to find RDF of one or
> more residue in vmd console.
> Thanks very much
> Best regards
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