VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Aug 14 2020 - 03:03:02 CDT

I think you will need to do a bit more than "just mention in your
manuscript". Your results [depending on what they are] would need a
reinterpretation.

The quickest way is to check the configuration script that you used to
actually set up your system.

https://www.ks.uiuc.edu/Research/namd/2.6/olddocs/ug/node26.html

As in the above link - the default is no.

The second quickest way would be to check the log file produced when
running the simulation.
The log file will have printed stuff like parameters used to set up PME.

Also as a reminder, you should always look at the configuration script and
the output logs to ensure that you are simulating stuff correctly and in
the right way. Depending on how you do this, your results may or may not be
different and will need to be interpreted accordingly.

On Fri, Aug 14, 2020 at 3:47 PM Debajeet Ghosh <fa29033_at_gmail.com> wrote:

> Hey,
> What if the PME value was set 'on' instead of 'yes'.
> I used it for simulation by mistake, I want to know if PME was used or not
> in my simulation so I can mention it in my manuscript. I believe both of
> them are boolean values.
> Thanks in advance,
> Debajeet.
>
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