VMD-L Mailing List

From: Ban Arn (ban.arn_at_gmail.com)
Date: Thu Feb 09 2012 - 16:17:48 CST

Dear John and Johan

Yes, Johan sorted out the problem of my input file.

Many Thanks for all your help.

Balaji

On Thu, Feb 9, 2012 at 8:23 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Balaji,
> Johan said that this ended up being an issue with the formatting
> of your own version of one of the files (not the original tutorial
> files), correct?. I assume that your problem is now solved. Let us know
> if there was anything else you needed there.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 08, 2012 at 09:59:22PM +0000, Ban Arn wrote:
> > Dear John
> > I got the error in both windows & linux machine.
> > In windows I tried with VMD version 1.8.7 & in linux machine its VMD v
> > 1.9.
> > Many Thanks
> > Balaji
> >
> > On Wed, Feb 8, 2012 at 9:18 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Balaji,
> > I just thought of something. Are you using a Windows machine to
> run
> > these scripts, or are you using MacOS X or a Unix (e.g. Linux)
> machine?
> > I ask because it is possible that if you're using Windows, one of
> the
> > scripts
> > may be incorrectly interpreting an end-of-file mark on a text file
> as an
> > input character from the file. I'm going to ask someone here to run
> > through
> > the same tutorial on our machines to see if they encounter a problem
> > like
> > you're having or not.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Mon, Feb 06, 2012 at 06:05:49PM +0000, Ban Arn wrote:
> > > Dear Axel
> > >
> > > I'm following the vmd SMD tutorial
> > >
> > "
> http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/node6.html
> "
> > >
> > > The array "f" is defined in load-traj.tcl script.
> > >
> > > Many Thanks
> > > Balaji
> > >
> > > On Mon, Feb 6, 2012 at 6:02 PM, Axel Kohlmeyer <
> akohlmey_at_gmail.com>
> > wrote:
> > >
> > > On Mon, Feb 6, 2012 at 12:57 PM, Ban Arn <ban.arn_at_gmail.com>
> > wrote:
> > > > Dear Axel
> > > >
> > > > Initially load this trajectory file, then define dt as 1
> and
> > pulling
> > > > velocity as 0.01 & Temperature (inclusing Boltzman
> constant) as
> > 0.6
> > > > and finally i'll use this script for calculating work done.
> > >
> > > i don't follow. where does the file come into play,
> > > and where do you define the "f" array.
> > >
> > > i am no mind reader, so i cannot give advice
> > > on stuff that i don't see.
> > >
> > > the error that you see, doesn't originate in the part of the
> code
> > that
> > > you quoted, but some *other* part, most likely where you
> define
> > "f".
> > > axel.
> > > >
> > > > Many Thanks
> > > > Balaji
> > > >
> > > >
> > > > On Mon, Feb 6, 2012 at 5:54 PM, Axel Kohlmeyer
> > <akohlmey_at_gmail.com>
> > > wrote:
> > > >>
> > > >> On Mon, Feb 6, 2012 at 12:51 PM, Ban Arn <
> ban.arn_at_gmail.com>
> > wrote:
> > > >> > Dear John & Axel
> > > >> >
> > > >> > Kindly find the attachment for reference file which I
> have
> > been
> > > using
> > > >> > for
> > > >> > the above script..
> > > >> >
> > > >> > The file has 11 columns 1st is time step, 2-6 columns
> are
> > > displacement
> > > >> > and
> > > >> > 7-11 columns are respective forces.
> > > >>
> > > >> i don't see the relation of this file with the piece of
> script
> > code.
> > > >>
> > > >> axel.
> > > >>
> > > >>
> > > >> >
> > > >> > Kindly advice.
> > > >> >
> > > >> > Many Thanks
> > > >> > Balaji
> > > >> >
> > > >> >
> > > >> >
> > > >> > On Mon, Feb 6, 2012 at 5:46 PM, Axel Kohlmeyer
> > <akohlmey_at_gmail.com>
> > > >> > wrote:
> > > >> >>
> > > >> >> On Mon, Feb 6, 2012 at 11:50 AM, Ban Arn
> > <ban.arn_at_gmail.com>
> > > wrote:
> > > >> >> > Dear VMD Users
> > > >> >> >
> > > >> >> > I'm using following script
> > > >> >> >
> > > >> >> > foreach l [array names f] {
> > > >> >> > set w($l) {}
> > > >> >> > set fsum 0
> > > >> >> > foreach ftemp $f($l) {
> > > >> >> > set fsum [expr $fsum + $ftemp * $v * $dt]
> > > >> >> > lappend w($l) $fsum
> > > >> >> > }
> > > >> >> > }
> > > >> >> >
> > > >> >> > for the calculation of work done for 10 simulations.
> > > >> >> >
> > > >> >> > While running the script it shows error as "missing
> > operand at
> > > _@_
> > > >> >> > in expression "0.25771 + _@_* 1 * 1"
> > > >> >> >
> > > >> >> > I'm not a tcl expert. Kinldy advice.
> > > >> >>
> > > >> >> ...and we don't know what you have in your "f" array.
> > > >> >> apparently no numbers.
> > > >> >>
> > > >> >> axel.
> > > >> >>
> > > >> >>
> > > >> >> >
> > > >> >> > Many Thanks
> > > >> >> > Balaji
> > > >> >> >
> > > >> >> >
> > > >> >>
> > > >> >>
> > > >> >>
> > > >> >> --
> > > >> >> Dr. Axel Kohlmeyer
> > > >> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> > > >> >>
> > > >> >> College of Science and Technology
> > > >> >> Temple University, Philadelphia PA, USA.
> > > >> >
> > > >> >
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> Dr. Axel Kohlmeyer
> > > >> akohlmey_at_gmail.com http://goo.gl/1wk0
> > > >>
> > > >> College of Science and Technology
> > > >> Temple University, Philadelphia PA, USA.
> > > >
> > > >
> > >
> > > --
> > > Dr. Axel Kohlmeyer
> > > akohlmey_at_gmail.com http://goo.gl/1wk0
> > >
> > > College of Science and Technology
> > > Temple University, Philadelphia PA, USA.
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>