From: emerson p l (emersonp90_at_gmail.com)
Date: Mon Feb 14 2022 - 12:50:13 CST

Thanks a lot for the comments, professors Dr. Giacomo Fiorin and Dr.
Philippe Bopp.

Running my vmd script with the flag "-dispdev text -e" solved my problem.

My vmd script worked correctly by running the command below:
path_to_vmd/vmd -dispdev text -e path_to_my_script/my_script.tcl

Thank you again for your precious time

Have a nice day!

Best regards,

Emerson.

Em seg., 14 de fev. de 2022 às 11:52, Giacomo Fiorin <
giacomo.fiorin_at_gmail.com> escreveu:

> Hi Emerson,
>
> On Mon, Feb 14, 2022 at 9:38 AM emerson p l <emersonp90_at_gmail.com> wrote:
>
>> Dear colleagues, I hope you are well.
>>
>> Ps: I am trying to send an email to VMD-L Mailing List, but my message
>> does not appear at
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/. If you have
>> already received my email before, please disregard this one. Sorry for the
>> spam.
>>
>> I'm a novice vmd user.
>>
>> I installed vmd 1.9.3 to run from the command line on a supercomputer I
>> use.
>>
>
> That version is now 5 years old, you're better off with a 1.9.4 alpha
> build.
>
>
>> I have 3 questions to solve and I would be grateful if some expert could
>> kindly help me.
>>
>> Well, vmd was installed in the directory
>> "/opt/pub/vmd/1.9.3/gcc/9.4.0/bin". When I go to this directory and run
>> ./vmd, vmd opens normally the console as it does on my personal desktop.
>>
>> *1)* I tried to execute a command to change directory (to the directory
>> where my trajectory files are, like "cd path") and apparently the console
>> hangs ("freeze", indeed). Do you have any suggestions as to what could
>> be causing this problem?
>> Ps: in the version installed on my desktop, the command works normally.
>> If I have to provide any supercomputer technical information, please let
>> me know.
>>
>
> This should be no different from going to that directory first through the
> shell, checking that you can "ls" the contentss from that same shell, and
> then launching vmd as "/opt/pub/vmd/1.9.3/gcc/9.4.0/bin/vmd" instead of
> "./vmd".
>
>
>>
>> *2) *Just a confirmation. To run a cmd script via an external file, do
>> I just have to open the vmd console and type "source filename"? Ps: the
>> intention is to know if the same procedure is feasible on a supercomputer.
>>
>
> Check out also the command line option "-e":
> https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node246.html#31667
>
>
>>
>> *3) *Is there any command (via the command line) to load a trajectory
>> and vmd waits to load all the frames of the trajectory file before doing
>> some calculation (like g(r))?
>>
>
> Check out the "waitfor" option to the "mol new" and "mol addfile" commands:
> https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/ug/node140.html
>
>
>>
>> Thanks in advance for your time,
>>
>> Best regards,
>>
>> Emerson.
>>
>