VMD-L Mailing List

From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Tue May 04 2021 - 12:45:55 CDT

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