VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Tue Oct 11 2022 - 19:45:48 CDT

Hi Norbert and Nick,

Thank you so much for your help. I have identified the second problem. For some reason, VMD had a problem with using psf when defining the mol variable. This is a warning that appeared in the VMD console:

Warning) Unable to ascertain filetype from filename 'psf'; assuming pdb.

When I changed the script to set mol [mol new J:/pc/Wildtype_100ns_Test1/run/Wildtype_100ns_Test1_QwikMD.psf waitfor all], the script works.

Do you happen to know how to alter the script to have the results written to a .dat file rather than just printed in the Tk console?

Additionally, is it possible to set a stride value for bigdcd? It does not seem like it, but I wanted to double check.

Best,
Christos
________________________________
From: Norbert Straeter <strater_at_bbz.uni-leipzig.de>
Sent: Tuesday, October 11, 2022 12:33 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: Re: vmd-l: Using BigDCD on Simulation Files Located on Mapped Network Drive


Unfortunately, the error messages in vmd are sometimes not so specific as for example a tcl error would be and you get no information, in which line the error occurs. Maybe the -debug option provides more information. I am not an expert in vmd. I guess, there were problems in loading the file. Try changing the file name to a wrong one and see if you get the same error. Copy the psf to the current working directory and see if that works.


Under windows I use vmd only via ubuntu for windows. I have a path like /mnt/c/Users/...


Sorry, I am not familiar with using vmd via windows/dos directly and cannot help with the path.




Am 11.10.2022 um 21:15 schrieb Efthymiou, Christos:
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
-------------------------------------------------------------------------------------------------------

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><mailto:strater_at_bbz.uni-leipzig.de>
Sent: Tuesday, October 11, 2022 12:05 PM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk><mailto:christos.dereschuk.20_at_ucl.ac.uk>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu><mailto: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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