VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 02 2010 - 08:43:42 CDT

dear parisa,

On Mon, Nov 1, 2010 at 10:40 PM, Parisa Akhski
<Parisa.Akhshi_at_chem.queensu.ca> wrote:
>
> Hi Jerome,
>
> Thanks for your reply. I really found your comments useful.
> Before writing any script to work on my own PC (second method as you
> mentioned), I would prefer to use the VMD text mode and use the command:
>
> vmd -dispdev text -e script.tcl
>
> I found the pbcunwrap.tcl script as provided in pbctools 2.5. However, after
> typing
>
> vmd -dispdev text -e pbcunwrap.tcl
>
> this is what I get:
>
> Info) VMD for LINUXAMD64, version 1.8.7a63 (March 31, 2009)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 7613MB (95%)
> Info) No CUDA accelerator devices found.
> Info) Creating CUDA device pool and initializing hardware...
> vmd >
>
> It seems that vmd does not do anything. I think it does not even start

why should it do anything. rule number one in scientific
computing is that just doing random stuff is the most
unproductive way to solve a problem. even in monte carlo
simulations randomness needs to be very well controlled
and balanced.

how to unwrap trajectories is a common theme on this mailing
list, so i suggest you first research the mailing list archives and
also study the documentation (vmd user's guide and the pbctools
plugin documentation at: http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ )

without that, you'll be wasting your and everybody else's time.

> loading the psf and dcd files. So, I tried this:
>
> vmd -dispdev text -psf filename.pdf -dcd filename.dcd
>
> and it loads both files successfully. Then I tried running pbcunwrap.tcl
> using several guessed commands but, none of them worked. Would you please
> help me if you have any idea?

why guess when there is documentation?

axel.

>
> Thanks,
> Parisa
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.