From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Sun Aug 10 2014 - 22:10:43 CDT
n 08/10/2014 09:59 PM, Hadi wrote:
> the algorithms that use bond constraints have
> their own limitations. I am not sure how NAMD addressed those issues about
> bond constraints.
The NAMD documentation quite clearly explains its use of well-established
constraint algorithms that have been in use since the early '80s.
Ubiquitously so for the last few decades (especially for water!) You're
essentially telling us that you, the great future Dr. Hadi Dinpajooh, have
found that these algorithms don't really work as advertised and that the
bulk of the MD work in the last few decades is flawed.
Here's more explanation from which you can rip quotes out of context,
though I'm seriously considering to stop replying if you do so because I'm
starting to doubt your good faith in this discussion.
http://en.wikipedia.org/wiki/Constraint_algorithm
> Molecule.C
> is just one subroutine that may or may not be related to the problems.
Maybe I should have made it clear this is the functionality responsible
for reading the bond section of the .psf file and applying parameters to
the list of bonds psf. It is critical to take note of what it does with
the counters; when encountering a bond with 0 force constant, it
effectively acts as if it never read it. When finished, it issues a
message saying:
"Warning: Ignored xxx bonds with zero force constants."
^^^^^^^
Since you're probably going to claim I'm "misunderstanding" the meaning of
the word "ignored", don't take my word for it, just generate a small water
box and simulate it for a bit with "rigidBonds all" with various
outrageous force constants. I can guaranteee you it will always gives the
same results except when setting it to 0.
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