VMD-L Mailing List

From: Nicholas Musolino (musolino_at_mit.edu)
Date: Thu Apr 08 2010 - 17:04:40 CDT

Dear Mr. Stone,

Thanks very much for your quick answer. I'll look into using xargs to work around the problems I'm experiencing.

Great to hear that DCD appending may come to future versions of VMD. My guess is that this could be useful to many users, especially once a person surmounts the VMD learning curve and starts scripting -- it's only natural to want to visualize what one is doing for debugging, or to save VMD analysis "runs" for recordkeeping purposes or for future analysis.

Thanks very much once again!

Nicholas

For the record, if anyone is interested in using xargs as suggested in the e-mail below, see this page:
http://www.mail-archive.com/uug-list@uug.byu.edu/msg19010.html

---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528

On Apr 8, 2010, at 5:18 PM, John Stone wrote:

>
> 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