VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 08 2010 - 16:18:41 CDT

Nicholas,
  You should be able to use "xargs" to pass long command lines beyond
what bash etc can handle and have it run catdcd to merge these as needed.
The catdcd code shouldn't have any hard-coded limits on command line args
AFAIK, so it's just what Linux/MacOS/etc will let you do. We don't have a
way to append an existing DCD file in VMD, but I'm working on addressing
this with future changes to the molfile plugins. Not all plugins will
ultimately allow appending, but some will, and DCD files are one of the
plugins that should work for this when I get it implemented.

Cheers,
  John

On Thu, Apr 08, 2010 at 04:50:04PM -0400, Nicholas Musolino wrote:
> Dear VMD mailing list,
>
> I have created a VMD script in which I change the coordinates (position/orientation) of a small molecule, along with two dihedral internal coordinates, in proximity to a surface. You could think of it as VMD-based docking.
>
> My approach so far has been to write separate, single-frame DCD files for each of these configurations, and then apply catDCD afterwards to combine all these single-frame files into a single DCD file after I'm done with VMD.
>
> What I would like to do is open for writing a *single DCD file* within VMD, and simply append frames to that. Is there any way to do this? Can I create a trajectory and "declare" new frames within VMD, and then use "animate write dcd ..."? I tried this latter approach but couldn't get it to work.
>
> My current approach becomes unworkable if I have more than ~1000 configurations, because catdcd can't accept too many arguments, nor can BASH commands like ls, rm, etc.
>
> Thanks in advance for any help anyone can offer!
>
> Nicholas Musolino
>
> ### Current approach: works, but creates large numbers of temporary DCD files
> ### Basic approach in VMD
> set timestep 0
> for {set u 0} {\$u <= 1.0} {set u [expr \$u+\$u_increment] } {
> for {set v 0} {\$v <= 1.0} { set v [expr \$v + \$v_increment]} {
> for { set psi1_count 1 } { \$psi1_count <= \$number_psi1_points } { incr psi1_count } {
> for { set psi2_count 1 } { \$psi2_count <= \$number_psi2_points } { incr psi2_count } {
> #
> # Manipulate coordinates of molecule here, based on current values of u, v, psi1, psi2
> #
> $allsel writedcd [ concat ${dcdoutputfile}_$timestep.dcd ]
> incr timestep
> }
> }
> }
> }
>
> #### After VMD exits, combine using catdcd
>
> ---------------------------------------------------------------------------
> Nicholas Musolino
> Ph.D. candidate, Department of Chemical Engineering, MIT
> musolino_at_mit.edu | 617-253-6675 | Room E19-528
>
>
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078