From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Tue Sep 29 2009 - 05:32:03 CDT
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 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
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.
All advices are highly appreciated
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