From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Aug 11 2014 - 14:08:41 CDT
On 08/11/2014 01:56 PM, Viswanath Pasumarthi wrote:
> considering a value of k=0 mean absence of spring (physical
> bond) between the respective atoms. It would have been easier to
> understand this mistake had there been an error message pointing to the
> choice of k value as zero.
But there *is* a message, and if you would have noticed/posted it, we
wouldn't have needed to have this long, marginally constructive
discussion. Look in your NAMD output for the following:
Warning: Ignored .* bonds with zero force constants.
Warning: Ignored .* angles with zero force constants.
Where .* is an integer.
> However, using rigidBonds constraints still
> required bond constraint values to be specified in the parameter file.
> This, as Kenno cautioned has turned into a flexible simulation, as
> covalent bonds involving hydrogen became more flexible at lower k values
> (1,2,5,10) and functioning decent at the values reported in modified TIP3P
> model.
I have to repeat that I tried and failed to reproduce this; my rigidBonds
simulations behave correctly for all force constants (even absurd values
such as 0.0001 or -10000) except zero. Most probably, there is an issue
with your psf and/or rigidBonds is not applied correctly. Which I have
been saying from the very beginning!
You probably need to try to use more detailed language (for example
"distances" or "force constants" rather than "values") when describing
your problem, and attach relevant input and output files to your posts,
else we'll never get anywhere.
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:06 CST