From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Mon Aug 11 2014 - 12:56:00 CDT
Thanks Kenno, Hadi and Axel for your valuable comments. Theoretically
speaking, 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. 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
> On Mon, Aug 11, 2014 at 12:16 AM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu> wrote:
>> On 08/10/2014 11:29 PM, Hadi wrote:
>> (*) "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),
>> the high-performance codes I'm familiar with deliberately avoid doing so
>> favor of a constraint algorithm.
> it is not only the arithmetic intensity that makes integrating the
> rotational degrees of freedom slow, but rather that this integration
> requires the use of a much shorter time step. please note, that time
> integration in euler angles is rarely done these days, because of the
> issue of their discontinuity is making the code extremely complex.
> usually codes use quaternions for time integration, as those are
> continuous. however, quaternions also have a well known problem of
> requiring different numerical accuracy depending on the orientation of
> the individual rigid bodies, and that can lead to quite significant
> errors as well, since we use floating point math with limited
> numerical accuracy.
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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