VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue May 04 2021 - 14:11:45 CDT

Hi Kelly,

How are you running the script?

If you use "only" the command line version of vmd to run this script or use
the GUI version in command line format - it should be fairly fast - with
the only bottleneck being write speed to disc.

Any other method, which you are hinting at, will cause overheads which may
not be helpful.
if you still want one write back and someone can make suggestions.

Regards,
/A

On Wed, May 5, 2021 at 2:23 AM Mcguire, Kelly <klmcguire_at_ucsd.edu> wrote:

> I have a DCD file with 5000 frames. I have a script that saves each frame
> as a PDB (shown below). This takes quite a bit of time to finish as you
> can imagine. Is there a way to run this in parallel with MPI (I don't have
> much experience with this) or on multiple CPUs on a node with 24 CPUs or
> multiple threads to speed up the process? I will need to do this with
> multiple DCD files in the future. Thanks!
>
>
> mol new ../../Aldolase-HMR.prmtop
> mol addfile ../../MD-1.nc waitfor all
>
> for {set i 1} {$i < 4999} {incr i} {
> [atomselect top all frame $i] writepdb $i.pdb
> }
>
>
>
> Dr. Kelly McGuire
> Postdoc
> Chemistry/Biochemistry Department
> Natural Science Building, 4104A, 4106A, 4017
>