VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 14 2022 - 08:52:14 CST

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.
>