From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Sun Aug 10 2014 - 23:16:19 CDT
On 08/10/2014 11:29 PM, Hadi wrote:
> Here is one citation regarding the flaws in the algorithms:
> THE DL POLY 2 USER MANUAL, i.e., section
> 2.5.7 Rigid Bodies and Rotational Integration Algorithms
If you read that carefully and think about it for a bit, you will find
that none of the problems listed there apply to the systems and constraint
schemes (bonds involving hydrogens only) that are the subject of the
current discussion. None, except for the following 2 points:
- Water is indeed defined as a triangle. While I have strong
reservations(*) about the authors' claim this is "slow", even if it were
justified to call it slow, this in no way supports your frivolous claim of
it being _inaccurate_.
- it is theoretically possible to overconstrain the rigid chloroform model
Viswanath is seeking to study, but that can trivially be avoided by not
making a beginner's mistake in the construction of the topology file.
(*) "slow" can only be defined relative to something else that's faster.
"Analytically" integrating rigid body rotations is computationally
surprisingly expensive (the trigonometric functions play a role there),
and the high-performance codes I'm familiar with deliberately avoid doing
so in favor of a constraint algorithm.
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