VMD-L Mailing List

From: Norbert Straeter (strater_at_bbz.uni-leipzig.de)
Date: Tue Oct 11 2022 - 14:33:49 CDT

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>
> *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
>>
> ----------------------------------------------