VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jun 13 2011 - 14:31:47 CDT

hi joe,

On Mon, Jun 13, 2011 at 2:36 PM, Joe Janicki <jjanickiduq_at_gmail.com> wrote:
> Greetings,
>
> I am trying to analyze .dcd trajectory files.
>
> Is there a way to automate the VolMap Tool to produce a .dx file for every
> frame in the trajectory?  I'm working with thousands of frames, and it would
> be unreasonable to do each frame individually.  I'd like two separate files

yes. the volmap command is exposed to the Tcl script interface:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node152.html

> for each frame- a .dx of the structure being studied and a .dx of the waters
> in the system.  Is it possible to write a script to automate this?  Any

yes. just make selections and use the -o flag to write to .dx files.

> pointers would be appreciated since I'm new to programming in VMD.

there are some examples in the VMD user's guide showing how to
loop over a trajectory for analysis.

> I would then like to edit the .dx files using another program.  I can save
> the output from that program in either .dx or .pdb format (in a single file
> made from the two files I previously described).
>
> From the thousands of .dx or .pdb files I generate from that program, is
> there a way to make a single file that I could load into VMD (similar to a
> trajectory file) that would have separate frames?  Essentially, I'd like to

that is not as simple. since volumetric data sets are not associated
with a trajectory file. but there is a way to script this using tcl callbacks.
check out this file.
http://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf

axel.

> overlay the original .dcd with the files I edited (a unique .dx or .pdb
> added to each frame of my original trajectory).  If not, writing a simple
> script would solve that, right?
>
> Any ideas on how to do (any) of this would be excellent.  I'll update if I
> figure out how to do any of this.
>
> Thank you,
> Joseph Janicki
> 

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