VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Jul 20 2004 - 01:29:03 CDT

>>> "BR" == Ben Roberts <Ben.P.Roberts_at_vcp.monash.edu.au> writes:

BR> Hi All,

hi,

BR> I have the results from a simulation as a CHARMm format DCD file, that is,
BR> containing Unit Cell information at each stage.

BR> Is it possible to use anything in NAMD or VMD to either:

BR> A) Obtain a radial distribution function, or

not yet automatically. an undergraduate(!) student in our department
is currently working on implementing several data analysis
features (principal component analysis, time correlation functions,
radial and spatial distribution functions, etc.) with VMD scripting.
he got very nice results so far and we are currently about to start
cleaning up and documenting it, so that it can be put up for download.

BR> B) At least produce unit cell dimensions from the DCD so I can put them in
BR> a PDB file and deal with them there?

assuming that your trajectory is loaded in molecule 0
you would get the unitcell data with something like

lassign [molinfo 0 get {a b c alpha beta gamma}] a b c alpha beta gamma
puts "$a $b $c $alpha $beta $gamma"

at the VMD prompt. if you step through the trajectory with

animate goto $frame

you can retrieve the unitcell data for the whole trajectory.
also, writing a small fortran program (the dcd format is (somewhat)
documented in several places) is also an option.

hope this helps,
     axel.

BR> Any advice would be appreciated.

BR> Thanks in advance and best regards,

BR> Ben

BR> ----------------------------------------------------------------------
BR> Benjamin P. Roberts, B.Sc.(Hons)
BR> Ph.D. Student

BR> Department of Medicinal Chemistry
BR> Victorian College of Pharmacy (Monash University)
BR> 381 Royal Parade, Parkville VIC 3052, Australia

BR> Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940
BR> ---------------------------------------------------------------------- 

--
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Axel Kohlmeyer       e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.