VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat May 23 2020 - 10:25:17 CDT

Hi Hemanth, if you are okay with using temporary DCD files, these can be
concatenated into a single one with catdcd, which can be called from the
VMD shell but is also a stand-alone code.

Giacomo

On Sat, May 23, 2020 at 9:01 AM HEMANTH H <hemanth.h_at_iitgn.ac.in> wrote:

> Sir,
>
> Thanks for your response. This is exactly what is happening with my
> script. It would be helpful if I could get some way to get it done.
>
> Best,
> Hemanth
>
> On Sat, 23 May 2020, 12:47 John Stone, <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> When you're writing out the DCD trajectory, you'll want to
>> add the options "waitfor all" to the end of the command
>> to ensure it completes fully. Also, VMD does not currently
>> allow you to append to the end of an existing trajectory, so
>> your script below likely simply overwrites whatever existing
>> file you have.
>>
>> Best,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, May 21, 2020 at 10:48:46AM +0530, HEMANTH H wrote:
>> > Dear All,
>> > I am trying to write out a few frames from my namd dcd file using the
>> > following tcl script. I am able to write out the frames to the dcd
>> file,
>> > but it is overwriting the previous dcd frame written. Any
>> suggestions are
>> > welcome.
>> > if {$nbasedist < 3.8} {
>> > if {$angle < 30.1 || $angle > 149.9}
>> > then {
>> > animate write dcd $stacked beg $f end $f
>> > }
>> > else
>> > {
>> > animate write dcd $unstacked beg $f end $f
>> > }
>> > }
>> > else
>> > {
>> > animate write dcd $unstacked beg $f end $f
>> > }
>> >
>> > }
>> > This the part of the script that fails.
>> > --
>> > Hemanth H 18310019
>> > Research Scholar
>> > IIT Gandhinagar
>>
>> --
>> NIH Center 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/
>>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin