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From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Tue May 04 2021 - 13:57:07 CDT
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Hi Kelly,
you could write a wrapper shell script that
creates multiple of such tcl script that only load 100 frames or
something each
...
set first xxx
set last yyy
mol new $psffile
mol addfile $dcdfile first $first last $last
This script you can then easily pass to a cluster batch system like
slurm (if you have this at hand):
for i in {1..10}; do
sbatch -c 1 -n 1 --wrap 'vmd -dispdev text -e script_id$i.tcl'
done
Cheers
René
On 5/4/2021 7:45 PM, Mcguire, Kelly 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
-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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