VMD-L Mailing List

From: HEMANTH H (hemanth.h_at_iitgn.ac.in)
Date: Sat May 23 2020 - 10:28:54 CDT

Thanks sir, I'll check them out.

On Sat, 23 May 2020, 20:55 Giacomo Fiorin, <giacomo.fiorin_at_gmail.com> wrote:

> 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
>