From: Hadi (dinpajooh_at_gmail.com)
Date: Thu Aug 07 2014 - 17:15:09 CDT
Again, I am sorry you misunderstood my statements. Your recent email
clearly shows that you were not aware of force constant problem until very
recently in this thread although it was the first response in the thread.
So I think you are partly mistaken by "your points are quite clear, and
I am happy you find my solution as the right one. In contrast to your
claim, I believe there are more complexities but I have no desire to
continue this thread except encouraging you to develop some force field in
NAMD with rigidBonds all option.
On Thu, Aug 7, 2014 at 1:08 PM, Kenno Vanommeslaeghe <
> On 08/07/2014 01:36 PM, Hadi wrote:
>> He misunderstood my points
> No, your points are quite clear, and inaccurate; see below.
> wanted to make me do an inappropriate action.
> Oh, so humility is "inappropriate" now? And here I thought I'd seen it all
> in this discussion...
> Now if one uses a force constant value of 0 in the parameter file:
>> The simulations become unstable.
> Viswanath (the person who started the thread) was wondering what one
>> should do in this case. So I suggested to use reasonable force constants.
> Again, let me emphasize that the simulations become unstable, etc. if one
>> does not use reasonable force constants. It does not matter whether one
>> uses SHAKE or SETTLE algorithms.
> You're still not fully getting it. rigidBonds effectively causes the force
> constant to be *ignored* in favor of constraining the distance. The
> confusion likely stems from the following two quirks:
> (1) I just discovered that if NAMD detects a force constant of EXACTLY
> ZERO, it will suppress rigidBonds for that degree freedom. I didn't know
> this because I always use the CHARMM parameter files. However, contrary to
> your claim, rigidBonds simulations will run stable and correctly with the
> most _unreasonable_ X-H force constants (including 0.0001 or 10000 or even
> -10000), just not 0.
> (2) the issue Viswanath had when using a high force constant was the
> *minimizer* crashing, *not* the MD simulation. I never used NAMD's
> minimizer (I do my system preparation in CHARMM), but Viswanath's anecdote
> suggests it does not support rigidBonds.
> So, to be fair, your solution of using the "fallback" values is actually
> the right one, *assuming* Viswanath did actually use rigidBonds (which we
> don't know!) As the "fallback" force constants are reasonable, they are not
> likely to destabilize the minimizer, and once the actual MD run starts, all
> that matters is that they are not zero. In the end, it's only your
> explanation of WHY your solution works that was incorrect. One might say
> that's a detail, but understanding exactly what one's simulation is doing
> is paramount to doing good science with it, and flinging around wildly
> inaccurate claims ticks off the list's regulars. If I were to falsely say:
> "your MC code is not correctly handling rigid molecules", wouldn't you feel
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