VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Tue Oct 11 2022 - 14:15:52 CDT

Hi Norbert,

Thank you so much for the correction. However, now I get the following error:

ERROR) No molecules loaded. mol new operates on one molecule only

Is there anything else that seems wrong in 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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I am having trouble finding examples online of providing the path to a psf or dcd file within a tcl script, so I appreciate any advice.

Best,
Christos

________________________________
From: Norbert Straeter <strater_at_bbz.uni-leipzig.de>
Sent: Tuesday, October 11, 2022 12:05 PM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Using BigDCD on Simulation Files Located on Mapped Network Drive

⚠ Caution: External sender

Hi Christos,

"set mol ..." not "set $mol ..."

Use $ only when you want to get value stored in the variable.

Best,

Norbert

Am 11.10.2022 um 20:33 schrieb Efthymiou, Christos:
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 

--
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Norbert Straeter                                      fon +49 (0)341-97-31311
Univ.-Prof. Dr. rer. nat.
Center for Biotechnology and Biomedicine
Institute of Bioanalytical Chemistry
Faculty of Chemistry and Mineralogy
Leipzig University
Deutscher Platz 5
04103 Leipzig, Germany                             strater_at_bbz.uni-leipzig.de<mailto:strater_at_bbz.uni-leipzig.de>
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