VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Tue Oct 11 2022 - 13:33:08 CDT

Hello,

I have run some large simulations with NAMD and the files are located on a mapped network drive on my Windows 10 computer. My simulation file is around 45 GB, so I would like to be able to use bigdcd to analyze the simulation. I have downloaded the script, and I am trying to calculate the center of mass from the example script.

Here is my script:
---------------------------------------------------------------------------------------------------
source C:/Users/Christos/Documents/VMD_Scripts/bigdcd.tcl

proc mycenter { frame } {
  global all
  puts "$frame: [measure center $all weight mass]"
}
set $mol [mol new psf J:/pc/Wildtype_100ns_Test1/run/Wildtype_100ns_Test1_QwikMD.psf waitfor all]
set all [atomselect $mol all]
$all global
bigdcd mycenter J:/pc/Wildtype_100ns_Test1/run/MD.dcd
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However, when I run this script, I get the following error:

can't read "mol": no such variable

How can I fix this error? I am providing the full path to the psf and dcd files that are located on my mapped network drive.

Best,
Christos