VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Sep 19 2009 - 10:14:22 CDT

On Fri, 2009-09-18 at 20:25 -0700, Goutham wrote:
>
> >...and again "it doesn't work" doesn't help at all!!
>
> package require signalproc
> gives an error message:
> can't find package signalproc

finally!!!

> However :
> package require specden
>
> loads fine without any error.
>
> Also the IRspec GUI works fine!

well, that can only mean, that you are
using an _obsolete_ version of VMD. with
the current version 1.8.7 of VMD the
the specden plugin has been moved from
the ispecgui to the signal proc package
as part of a large collection of tools to
work on data sets. there is more to come
for the next versions of VMD (if i can
find the time).

> -----
>
>
> doesn't work how? is there an error message? if yes, which
> one?
> which version of VMD do you have? which platform?
>
>
>
> I have tried VMD1.8.4, VMD1.8.6 on linux. The above mentioned specden
> package loads up on my Mac running VMD1.8.6.

well, there you go. you cannot expect me to read your mind
and know that you are using a version of VMD that is not
up-to-date. nevertheless. the "package require specden" only
loads the spectral density calculator, even if it has become
part of the signalproc package. package require signalproc is
provided as a convenience; its only job is to load all integrated
subpackages. please have a closer look at the docs.

> i am confused! how can it make your life easy, if it doesn't
> work for you???
>
>
>
> When I tried using the IRspecGUI on the linux machine, it worked fine.
> I computed spectral density from the veldcd, and the peaks were as I
> expected. Which is the part that works. The script doesn't work
> though.

it does work. it _has_ to work (if you use the specden package), because
all what the GUI does is to compile the command line arguments and
then call the specden command. the example scripts are simplified
variants of the GUI plugin.

> However teh actual case for which I want to compute the spectrum, is
> very big in size (8GB), and my computer freezes when I load the dcd
> file. I am thinking if I tried a script version, I probably won't have
> that issue.

this is a reasoning that i cannot follow. if your machine freezes with
an 8GB file, then you are running out of memory (how much do you have?).
please note that to call the specden plugin, you have to first compile
a tcl list of your data. this will have _additional_ memory requirements
that are more than double that of the 8GB that your dcd file has in
size, since tcl internally stores all floating point numbers in double
precision (i.e. at double the storage). together with the overhead for
linked lists and the auto-converting data type that tcl uses, you may
need physical memory in excess of 40GB just to be able to run the whole
data set in one go.

in these cases it is highly advisable to process that data in pieces
or write a custom analysis tool that avoids the frequent copying. in
general for processing ultra-large data sets, one always has to consider
the extra overhead from tcl/python scripting.

cheers,
   axel.

>
>
> Thanks
> Goutham
>
>
>
>
>
>
>
>
>
>
> axel.
>
>
> >
> > Best
> > Goutham
> >
> >
> >
> >
> >
> > On Fri, Sep 18, 2009 at 1:36 PM, Axel Kohlmeyer
> <akohlmey_at_gmail.com> wrote:
> >>
> >> On Fri, Sep 18, 2009 at 3:53 PM, Goutham
> <gouthambs_at_gmail.com> wrote:
> >> > Hey All,
> >> >
> >> > Does any of you know of any packages to calculate
> (velocity)
> >> > auto-correlation? I saw a "signalproc" package here:
> >> >
> >> > http://www.ks.uiuc.edu/Research/vmd/plugins/signalproc/
> >> >
> >> > But this somehow doesn't work. Will be nice if any one
> can give me
> >> > pointers
> >> > to it.
> >>
> >> hey goutham,
> >>
> >> _what_ doesn't work? and _how_ does it not work?
> >> just saying that something doesn't work is not very
> helpful.
> >> more often than not these problems are a cases of PEBCAC.
> >>
> >> the specden command in that package computes spectral
> >> densities directly from convoluted data and can do this
> with
> >> any data, including velocities. but you don't have the
> intermediate
> >> VACF but assemble the data directly in fourier space. this
> is
> >> very adventageous for large data sets and removes the
> arbitrariness
> >> in traditional VACF based spectraldensities (and avoids the
> O(N**2)
> >> scaling with correlation length to boot). i have a
> truckload of those
> >> spectra lying around on my harddrive, and they all look
> great and
> >> have worked fine. ;)
> >>
> >> other than that, programming a VACF directly is
> embarrassingly
> >> simple in VMD, it just is dog slow.
> >>
> >> cheers,
> >> axel.
> >>
> >> >
> >> > Best
> >> > Goutham
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> >> Institute for Computational Molecular Science
> >> College of Science and Technology
> >> Temple University, Philadelphia PA, USA.
> >
> >
>
>
>
>
> --
>
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
> 

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