From: Peter Freddolino (
Date: Fri Aug 14 2020 - 07:27:01 CDT

In general 'yes', 'on', and 'true' for boolean options *in NAMD* will all
behave equivalently. Here is the relevant code from the config file parser

// convert from a string to Bool; returns 1(TRUE) 0(FALSE) or -1(if unknown)
int ParseOptions::atoBool(const char *s)
   if (!strcasecmp(s, "on")) return 1;
   if (!strcasecmp(s, "off")) return 0;
   if (!strcasecmp(s, "true")) return 1;
   if (!strcasecmp(s, "false")) return 0;
   if (!strcasecmp(s, "yes")) return 1;
   if (!strcasecmp(s, "no")) return 0;
   if (!strcasecmp(s, "1")) return 1;
   if (!strcasecmp(s, "0")) return 0;
   return -1;

With that said, it is of course good to confirm in your log file that PME
is active, and it is *always* good advice to double/triple/quadruple check
your inputs to avoid cases like this.


On Fri, Aug 14, 2020 at 5:43 AM Ashar Malik <> wrote:

> 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.
> 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 <> 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.
>> [image: Mailtrack]
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>> notified by
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>> <> 08/14/20,
>> 12:40:44 PM