VMD-L Mailing List

From: morten østergaard jensen (mjensen_at_memphys.sdu.dk)
Date: Tue Aug 22 2006 - 10:02:19 CDT

Being short of memory, you can visualize a big trajectory if that's what
you want. Using bigdcd.tcl as of Peter's previous mail, you'll be able
to play the whole trajectory, at least frame by frame as: 

----
proc anim {frame} {
    animate goto $frame; display update
    #you might obvoiously do analysis calculation here as well.
}
mol load .... my_system. ... (whatever format, e.g., a psf / pdb pair of 
files).
bigdcd anim my_big_trajectory.dcd
----
(If you happen to not use dcd's, "animate read..." within bigdcd.tcl can 
be trivially modified to acccept VMD's other supported formats).
Good luck -
Morten
>On Tue, 22 Aug 2006, Lechuga, Javier wrote:
>
>JL> Hello,
>JL>  
>
>JL> When trying to open big files with VMD I am having memory allocation
>JL> errors. Is there a way to bypass this?. Molecular dynamics usually
>JL> get to give huge result files.
>
>you have a number of options:
> - buy more memory for your machine
> - save data less frequently
> - load only parts of your trajectory
> - use a stride > 1 when loading trajectories
> - use the bigdcd script when running analysis functions
>
>cheers,
>    axel.
>
>
>JL>  
>JL> Thank you
>JL> 
>
>  
>