Re: g(r) GUI Plugin problem

From: Axel Kohlmeyer (
Date: Tue Sep 29 2009 - 14:02:16 CDT

dear branko,

On Tue, Sep 29, 2009 at 4:32 AM, Branko <> wrote:
> Dear all,

first off, please report problems with VMD to the VMD mailing list
and not the NAMD mailing list. you chances to get a useful answer
will increase manyfold.

> I was trying to calculate RDF from trajectory of ~ 5 ns (total 2500
> framesminus equilibration). Trajectory comprises small molecule solvated by
> n-octanol/water cluster. I am interested, at first, for RDF “between”
> carboxylate H of small molecule and O from OH of n-octanol. After successful
> psf and dcd importing in VMD (1.8.6), choosing Analysis\Rad. Pair…\ and

please first update to version 1.8.7. the measure gofr command in 1.8.6
has some (minor) bugs that will result in inaccurate results. most of the
time the inaccuracy will not matter much, but still...

> typing necessary information in graphical interface script failed to give
> nay reasonable results. For example setting Frames first: 116 (end of
> equilibration) last 2499 (problem with 2500, not important), step 1, delta r
> 0.1, max r 4 or any number 4-9 and checking use PBC script failed to process
> any frame and output is 0.0 for all distances (both columns). I suppose that
> selection of atoms (assignation of atoms labels from which RDF should be
> calculated) can be wrong.

the gofrgui plugin strictly follows the GI-GO principle (= garbage in,
garbage out).
you have to debug your selections first. this is hard to do from remote,
but you can create a visualization where you overlay a lines representation for
all atoms with a VDW or CPK representation for your selection and then
you can see if your selection hits the correct atoms.

> Small molecule is “chain” A, segment 1, residue UNK1, and desired atom for
> this calculation is (name) H30
> Solvent cluster is “chain” S, segment 2, residue OCT (desired atom of any
> OCT molecule in proximity should be accounted), and desired atom for this
> calculation is O24.
> So, how can I assign those atoms in selection 1 and selection 2.
> Also please explain me what is difference between index and serial,
> providing that two desired atoms belongs to two segments.

please have a closer look at the VMD documentation.


> All advices are highly appreciated
> Branko

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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