VMD-L Mailing List

From: Georcki Ropon (groponp_at_gmail.com)
Date: Thu Oct 13 2022 - 14:31:37 CDT

Hi Christos,

It is a syntax erro mol, it defined as variable , in set $mol, change it by set mol only.

Best,

Geo

Obtener Outlook para iOS<https://urldefense.com/v3/__https://aka.ms/o0ukef__;!!DZ3fjg!5YhtDi_zDDdPisVtOgOGhOsWFs_KtcR2h7Pt_nqE6cets_XBeX_PPYpMzHiOfHOA5VfiH5xGCvu0CheQ$ >
________________________________
De: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> en nombre de Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
Enviado: Tuesday, October 11, 2022 1:33:08 PM
Para: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Asunto: vmd-l: Using BigDCD on Simulation Files Located on Mapped Network Drive

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
------------------------------------------------------------------------------------------------------

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