VMD-L Mailing List

From: Norbert Straeter (strater_at_bbz.uni-leipzig.de)
Date: Wed Oct 12 2022 - 03:02:29 CDT

Hi Christos,

You can redirect the output of a script or program to a file:

my_script.com > output.log

This will work under unix and dos.

Under unix to file and console: my_script.com | tee output.log

I think one will need to change the bigdcd script to implement a stride
value, to implement a counter that is incremented after each frame is
read and only call the analysis subroutine if this counter can be
divided by the stride value to give an integer number. Or call the
analysis subroutine when counter == stride reset the counter to 0.  This
requires to work yourself into tcl and the bigdcd script, which will
require some time.

Alternatively use catdcd bevore running the bigdcd script.

Best regards,

Norbert

Am 12.10.2022 um 02:45 schrieb Efthymiou, Christos:
> 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
> ------------------------------------------------------------------------
>